Plant retroelements and methods related thereto

ABSTRACT

The present invention provides plant retroelements useful as molecular tools. In one embodiment, the present invention provides nucleic acids encoding gag, pol and/or env genes of plant retroelements. The elements can be used, among other uses, as building blocks of other constructs, tools to find other nucleic acid sequences and tools to transfer nucleic acid into cells.

[0001] This application claims priority to U.S. Provisional Patent Application Serial No. 60/087125, filed May 29, 1998.

[0002] This application is a continuation (and claims the benefit of priority under 35 U.S.C. §120) of U.S. Ser. No. 09/965,553, filed Sep. 27, 2001, which is a divisional of U.S. Ser. No. 09/322,478, filed May 28, 1999, now U.S. Pat. No. 6.331,662, which claims priority to U.S. Provisional Patent Application Serial No. 60/087,125, filed May 29, 1998, all of which are incorporated herein by reference in their entirety.

[0003] The present invention was funded, in part, by the United States Department of Agriculture, Contract Number IOW03120; the United States Government may have certain rights in the invention.

FIELD OF THE INVENTION

[0004] The present invention provides plant retroelements and methods related to plant retroelements. The invention involves techniques from the fields of: molecular biology, virology, genetics, bioinformatics, and, to a lesser extent, other related fields.

BACKGROUND OF THE INVENTION

[0005] The eukaryotic retrotransposons are divided into two distinct classes of elements based on their structure: the long terminal repeat (LTR) retrotransposons and the LINE-like or non LTR elements. Doolittle et al. (1989) Quart. Rev. Biol. 64: 1-30; Xiong and Eickbush (1990) EMBO J 9: 3353-3362. These element classes are related by the fact that each must undergo reverse transcription of an RNA intermediate to replicate, and each generally encodes its own reverse transcriptase. The LTR retrotransposons replicate by a mechanism which resembles that of the retroviruses. Boeke and Sandmeyer, (1991) Yeast transposable elements. In The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by J. Broach, E. Jones and J. Pringle, pp. 193-261. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. They typically use a specific tRNA to prime reverse transcription, and a linear cDNA is synthesized through a series of template transfers that require redundant LTR sequences at each end of the element mRNA. This all occurs within a virus-like particle formed from proteins encoded by the retrotransposon mRNA. After reverse transcription, an integration complex is organized that directs the resulting cDNA to a new site in the genome of the host cell.

[0006] Phylogenetic analyses based on reverse transcriptase amino acid sequences resolve the LTR retrotransposons into two families: the Ty3/gypsy retrotransposons (Metaviridae), and the Ty1/copia elements (Pseudoviridae). Boeke et al., (1998) Metaviridae. In Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Springer-Verlag, New York; Boeke et al. (1998) Pseudoviridae. In Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Springer Verlag, New York.; Xiong and Eickbush (1990) EMBO J. 9: 3353-3362. Although distinct, Ty3/gypsy elements are more closely related to the retroviruses than to the Ty1/copia elements. They also share a similar genetic organization with the retroviruses, principally in the order of integrase and reverse transcriptase in their pol genes. For the Ty3/gypsy elements, reverse transcriptase precedes integrase, and this order is reversed for the Ty1/copia elements. In addition, some Ty3/gypsy elements have an extra open reading frame (ORF) similar to retroviral envelope (env) proteins, which is required for viral infectivity. The Drosophila melanogaster gypsy retrotransposons encode an env-like ORF and can be transmitted between cells. Kim et al. (1994) Proc. Natl. Acad. Sci. USA 91: 1285-1289; Song et al. (1994) Genes & Dev. 8: 2046-2057. Thus there are two distinct lineages of infectious LTR retroelements, the retroviruses and those Ty3/gypsy retrotransposons that encode envelope-like proteins. The Ty3/gypsy elements have been divided into two genera, the metaviruses and the errantiviruses, the latter of which include all elements with env-like genes. Boeke et al., (1998) Metaviridae. In Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Springer-Verlag, New York

[0007] In plants, retrotransposons have been extremely successful. Bennetzen (1996) Trends Microbiol. 4: 347-353; Voytas (1996) Genetics 142: 569-578. The enormous size of many plant genomes demonstrates a great tolerance for repetitive DNA, a substantial proportion of which appears to be composed of retrotransposons. Because of their abundance, retrotransposons have undoubtedly influenced plant gene evolution. They can cause mutations in coding sequences (Grandbastien et al. (1989) Nature 337: 376-380; Hirochika et al. (1996) Proc. Natl. Acad. Sci. USA 93: 7783-7788; Purugganan and Wessler (1994) Proc. Natl. Acad. Sci. USA 91: 11674-11678), and the promoter regions of some plant genes contain relics of retrotransposon insertions that contribute transcriptional regulatory sequences. White et al. (1994) Proc. Natl. Acad. Sci. USA 91: 11792-11796. Retrotransposons also generate gene duplications: Repetitive retrotransposon sequences provide substrates for unequal crossing over, and such an event is thought to have caused a zein gene duplication in maize. White et al. (1994) Proc. Natl. Acad. Sci. USA 91: 11792-11796. Occasionally, cellular mRNAs are reverse transcribed and the resultant cDNA recombines into the genome giving rise to new genes, or more frequently, cDNA pseudogenes. Maestre et al. (1995) EMBO J. 14: 6333-6338. The transduction of gene sequences during reverse transcription, which produced the oncogenic retroviruses, has also been documented to occur for a plant retrotransposon (Bureau et al. (1994) Cell 77: 479-480.; Jin and Bennetzen (1994) Plant Cell 6: 1177 1186); a maize Bs1 insertion in Adh1 carries part of an ATPase gene and is the only known example of a retrotransposon-mediated gene transduction event.

[0008] Plant genomes encode representatives of the two major lineages of LTR retrotransposons that have been identified in other eukaryotes. Among these are numerous examples of Ty1/copia elements (e.g. Konieczny et al. (1991) Genetics 127: 801-809; Voytas and Ausubel (1988) Nature 336: 242-244; Voytas et al. (1990) Genetics 126: 713-721) Also prevalent are Ty3/gypsy elements, which are members of the genus Metaviridae (Smyth et al. 1989; Purugganan and Wessler 1994 Proc. Natl. Acad. Sci. USA 91: 11674-11678; Su and Brown 1997). As stated above, the metaviruses do not encode an envelope protein characteristic of the retroviruses. It has been suggested that some plant retrovirus-like elements may have lost, or not yet gained, genes such as the envelope gene required for cell-to-cell transmission (Bennetzen (1996) Trends Microbiol. 4: 347-353). As one group of researchers described the uncertainty, “[s]ince genes encoding ENV [envelope] functions are very heterogeneous at the sequence level and difficult to identify by homology even between retroviruses, the possibility cannot be completely excluded at the present time that the 3′ ORF of Cyclops [the retrotransposon described in the paper] is, in fact, an env gene and, hence, Cyclops is a retrovirus or a descendant of one.” Chavanne et al. (1998) Plant Molecular Biol 37: 363-375.

[0009] Citation of the above documents is not intended as an admission that any of the foregoing is pertinent prior art. All statements as to the date or representation as to the contents of these documents is based on subjective characterization of information available to the applicant, and does not constitute any admission as to the accuracy of the dates or contents of these documents.

SUMMARY OF THE INVENTION

[0010] In general, the present invention provides materials, such as nucleic acids, vectors, cells, and plants (including plant parts, seeds, embryos, etc.), and methods to manipulate the materials. In particular, molecular tools are provided in the form of retroelements and retroelement-containing vectors, cells and plants. The particular methods include methods to introduce the retroelements into cells, especially wherein the retroelements carries at least one agronomically-significant characteristic. The best mode of the present invention is a particular method to transfer agronomically-significant characteristics to plants wherein a helper cell line which expresses gag, pol and env sequences is used to enable transfer of a secondary construct which carries an agronomically-significant characteristic and has retroelement sequences that allow for replication and integration.

[0011] In one embodiment, there are provided isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant retroelement and comprises a nucleic acid sequence selected from the group consisting of:

[0012] (a) a nucleic acid sequence which is a plant retroelement primer binding site and which has more than 95% identity to SEQ ID NO 2, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0013] (b) a nucleic acid sequence which is at least a portion of a plant retroelement envelope sequence and which has more than 50% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0014] (c) a nucleic acid sequence which is at least a portion of a plant retroelement gag sequence and which has more than 50% identity to SEQ ID NO 7, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0015] (d) a nucleic acid sequence which is at least a portion of a plant retroelement integrase sequence and which has more than 70% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0016] (e) a nucleic acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and which has more than 70% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0017] (f) a nucleic acid sequence which is at least a portion of a plant retroelement protease sequence and which has more than 50% identity to SEQ ID NO 13, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0018] (g) a nucleic acid sequence which is at least a portion of a plant retroelement RNAseH sequence and which has more than 70% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0019] (h) a nucleic acid sequence which is at least a portion of a plant retroelement sequence and which has more than 50% identity to SEQ ID NO 17, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0020] (i) a nucleic acid sequence which is selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17.

[0021] (j) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement envelope sequence and has more than 30% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0022] (k) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement gag sequence and has more than 30% identity to SEQ ID NO 8, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0023] (l) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement integrase sequence and has more than 75% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0024] (m) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and has more than 79% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0025] (n) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement protease sequence and has more than 55% identity to SEQ ID NO 14, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0026] (o) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement RNAseH sequence and has more than 90% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0027] (p) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement sequence and has more than 40% identity to SEQ ID NO 18, wherein said identity can be determined using the DNAsis computer program;

[0028] (q) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18;

[0029] (r) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; and

[0030] (s) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); a nucleic acid sequence of (e); a nucleic acid sequence of (f); a nucleic acid sequence of (g); a nucleic acid sequence of (h); a nucleic acid sequence of (i); a nucleic acid sequence of (j); a nucleic acid sequence of (k); a nucleic acid sequence of (l); a nucleic acid sequence of (m); a nucleic acid sequence of (n); a nucleic acid sequence of (o); a nucleic acid sequence of (p); a nucleic acid sequence of (q); and a nucleic acid sequence of (r).

[0031] Seeds and plants comprising a nucleic acid as above are particularly provided. Nucleic acid molecules as above which comprise gag, pot and env genes and which comprise adenine-thymidine-guanidine as the gag gene start codon are also particularly provided. Those which comprise gag, pol and env genes, the adenine-thymidine-guanidine as the gag gene start codon, and which further comprises SEQ ID NO 4 are also provided.

[0032] Plant envelope sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant envelope sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0033] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0034] (b) a nucleic acid sequence which encodes SEQ ID NO 5;

[0035] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0036] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 6;

[0037] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 6; and

[0038] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0039] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant envelope proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant envelope protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0040] Plant integrase sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant integrase sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0041] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0042] (b) a nucleic acid sequence which encodes SEQ ID NO 9;

[0043] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0044] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 10;

[0045] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 10; and

[0046] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0047] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant integrase proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant integrase protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0048] Plant reverse transcriptase sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant reverse transcriptase sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0049] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0050] (b) a nucleic acid sequence which encodes SEQ ID NO 11;

[0051] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0052] (d) a nucleic acid sequence which-encodes amino acid sequence SEQ ID NO 12;

[0053] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 12; and

[0054] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0055] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant reverse transcriptase proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant reverse transcriptase protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0056] Plant RNAseH sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant RNAseH sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0057] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0058] (b) a nucleic acid sequence which encodes SEQ ID NO 15;

[0059] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 95% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0060] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 16;

[0061] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 16; and

[0062] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0063] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant RNAseH proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant RNAseH protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0064] Plant retroelement sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant retroelement sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0065] (a) a nucleic acid sequence which has more than 95% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0066] (b) a nucleic acid sequence which is selected from the group consisting of: SEQ ID NO 2; SEQID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17;

[0067] (c) a nucleic acid sequence which encodes an amino acid sequence which has more than 90% identity to an amino acid sequence selected from the group consisting of SEQID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; SEQ ID NO 18, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0068] (d) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18;

[0069] (e) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; and

[0070] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0071] Nucleic acid molecule as above, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those nucleic acid molecules as described wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content and those wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0072] Seeds and plants comprising a nucleic acid molecule as described are also preferred. More preferred are plants as described, wherein the plant is selected from the group consisting of: soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper, melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber; pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower; peanut; and olive. Most preferred are plants as described which are soybean plants.

[0073] Plant retroelements comprising an amino acid sequence encoded by a nucleic acid sequence described are also provided. Plant cells comprising a nucleic acid molecule described herein, as well as plant retroviral proteins encoded by nucleic acid molecules described herein are provided.

[0074] Moreover, methods to transfer nucleic acid into a plant cell, comprising contacting a nucleic acid molecule of the present invention with at least one plant cell under conditions sufficient to allow said nucleic acid molecule to enter at least one cell of said plant are provided. In particular there is provided, methods to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroelement of the present invention to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic. Methods as described, wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content and those wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0075] Plant retroelement sequences comprising specialized signals, and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, comprising a nucleic acid sequence selected from the group consisting of:

[0076] (a) a nucleic acid sequence which has more than 95% identity to SEQ ID NO 2; wherein said identity can be determined using the DNAsis computer program and default parameters;

[0077] (b) a nucleic acid sequence which is SEQ ID NO 2;

[0078] (c) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 4; and

[0079] (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).

[0080] Plant retroelements as described above, which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those methods wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content and those wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0081] Preferred are plant retroviral particles comprising an isolated retroelement as described, and seeds and plants comprising the retroelements as described. More preferred plants include soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower, alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper; melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber; pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower, peanut; and olive. Soybean is most preferred.

[0082] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroelement as described with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell. Methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroelement as described with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell are also preferred. Those methods wherein the plant retroelement is contacted with said cell via a plant retroviral particle described herein are preferred.

[0083] Plant retroviruses are also provided. In particular, plant retroviral particles comprising a plant-derived retrovirus envelope protein are provided. Plant retroviral particles comprising a plant-derived retrovirus envelope protein and which further comprise a plant retroviral protein selected from the group consisting of: plant-derived integrase; plant derived reverse transcriptase; plant-derived gag; and plant-derived RNAseH are preferred.

[0084] Plant retroviral particles comprising specialized retroviral proteins, and cells, seeds, embryos and plants which comprise the retroviral particles are provided. Preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0085] (a) a nucleic acid sequence comprising (i) a nucleic acid sequence which encodes at least one plant retroviral envelope protein, and (ii) a nucleic acid sequence which has more than 60% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0086] (b) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence (a);

[0087] (c) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid sequence of (a); and

[0088] (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).

[0089] In particular, there are provided plant retroviral particles, wherein said nucleic acid sequence as described in (a) comprises a plant envelope nucleic acid specifically mentioned in claim 6 is preferred. Those particles which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred.

[0090] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0091] More preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0092] (a) a nucleic acid sequence which has more than 80% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0093] (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15;

[0094] (c) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b);

[0095] (d) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); and

[0096] (e) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); and a nucleic acid sequence of (d).

[0097] Nucleic acids as above, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those nucleic acids wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content. Also more preferred are those isolated nucleic acid molecule as described, wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0098] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0099] Also preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0100] (a) a nucleic acid sequence which has more than 60% identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0101] (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31;

[0102] (c) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b);

[0103] (d) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); and

[0104] (e) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); and a nucleic acid sequence of (d).

[0105] Plant retroviral particles as described above, which further comprises an envelope-encoding nucleic acid sequence specifically described herein are preferred. Preferred are those retroviral particles which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic.

[0106] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0107] “Allelic variant” is meant to refer to a full length gene or partial sequence of a full length gene that occurs at essentially the same locus (or loci) as the referent sequence, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions).

[0108] By “agronomically-significant” it is meant any trait of a plant which is recognized by members of the agricultural industry as desirable.

[0109] “Fragment” is meant to refer to any subset of the referent nucleic acid molecule.

[0110] By “plant” it is meant one or more plant seed, plant embryo, plant part or whole plant. The plant may be an angiosperm (monocot or dicot), gymnosperm, man-made or naturally-occurring.

[0111] By “proteins” it is meant any compounds which comprise amino acids, including peptides, polypeptides, fusion proteins, etc.

[0112] Moreover, for the purposes of the present invention, the term “a” or “an” entity refers to one or more of that entity; for example, “a protein” or “a nucleic acid molecule” refers to one or more of those compounds or at least one compound. As such, the terms “a” (or “an”), “one or more” and “at least one” can be used interchangeably herein. It is also to be noted that the terms “comprising”, “including”, and “having” can be used interchangeably. Furthermore, a compound “selected from the group consisting of” refers to one or more of the compounds in the list that follows, including mixtures (i.e., combinations) of two or more of the compounds. According to the present invention, an isolated, or biologically pure, protein or nucleic acid molecule is a compound that has been removed from its natural milieu. As such, “isolated” and “biologically pure” do not necessarily reflect the extent to which the compound has been purified. An isolated compound of the present invention can be obtained from its natural source, can be produced using molecular biology techniques or can be produced by chemical synthesis. Lastly, “more than” and “greater than” are interchangeable, and when used to modify a percent identity, ie. “more than 90% identity”, mean any increment to 100%, so long as the increment were greater than the percentage specifically named. In the example of “more than 90% identity”, the term would include, among all other possibilities, 90.00001, 93.7, 98.04 and 99.0827 and 100%.

[0113] The following is a summary of the sequence listing, as a convenient reference. SEQ ID NO Description  1 specialized primer binding site version 1  2 specialized primer binding site version 2  3 specialized polypurine tract  4 targeting sequence  5 NA generic envelope  6 AA of 5  7 NA of generic gag  8 AA of 7  9 NA of generic integrase 10 AA of 9 11 NA of generic reverse transcriptase 12 AA of 11 13 generic protease 14 AA of 13 15 generic RNAseH 16 AA of 15 17 generic retroelement 18 AA of 17 19 NA calypso 1-1 20 NA calypso 1-2 21 NA calypso 1-3 22 NA calypso 2-1 23 NA calypso 2-2 24 NA athila env 25 NA cyclops env 26 NA athila integrase 27 NA athila reverse transcriptase 28 NA athila RNAseH 29 NA cyclops reverse transcriptase 30 NA cyclops RNAseH 31 NA cyclops integrase 32 NA calypso envelope 33 NA calypso RNAseH 34 NA calypso reverse transcriptase 35 NA calypso integrase 36 Primer binding site A 37 Primer binding site B 38 Primer binding site minimum 39 Primer binding site extended 40 polypurine tract A 41 polypurine tract B

DETAILED DESCRIPTION OF THE INVENTION

[0114] In one embodiment, there are provided isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant retroelement and comprises a nucleic acid sequence selected from the group consisting of:

[0115] (a) a nucleic acid sequence which is a plant retroelement primer binding site and which has more than 95% identity to SEQ ID NO 2, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0116] (b) a nucleic acid sequence which is at least a portion of a plant retroelement envelope sequence and which has more than 50% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0117] (c) a nucleic acid sequence which is at least a portion of a plant retroelement gag sequence and which has more than 50% identity to SEQ ID NO 7, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0118] (d) a nucleic acid sequence which is at least a portion of a plant retroelement integrase sequence and which has more than 70% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0119] (e) a nucleic acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and which has more than 70% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0120] (f) a nucleic acid sequence which is at least a portion of a plant retroelement protease sequence and which has more than 50% identity to SEQ ID NO 13, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0121] (g) a nucleic acid sequence which is at least a portion of a plant retroelement RNAseH sequence and which has more than 70% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0122] (h) a nucleic acid sequence which is at least a portion of a plant retroelement sequence and which has more than 50% identity to SEQ ID NO 17, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0123] (i) a nucleic acid sequence which is selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17.

[0124] (j) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement envelope sequence and has more than 30% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0125] (k) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement gag sequence and has more than 30% identity to SEQ ID NO 8, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0126] (l) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement integrase sequence and has more than 75% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0127] (m) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and has more than 79% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0128] (n) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement protease sequence and has more than 55% identity to SEQ ID NO 14, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0129] (o) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement RNAseH sequence and has more than 90% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0130] (p) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement sequence and has more than 40% identity to SEQ ID NO 18, wherein said identity can be determined using the DNAsis computer program;

[0131] (q) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18;

[0132] (r) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; and

[0133] (s) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); a nucleic acid sequence of (e); a nucleic acid sequence of (f); a nucleic acid sequence of (g); a nucleic acid sequence of (h); a nucleic acid sequence of (i); a nucleic acid sequence of (j); a nucleic acid sequence of (k); a nucleic acid sequence of (l); a nucleic acid sequence of (m); a nucleic acid sequence of (n); a nucleic acid sequence of (o); a nucleic acid sequence of (p); a nucleic acid sequence of (q); and a nucleic acid sequence of (r).

[0134] Seeds and plants comprising a nucleic acid as above are particularly provided. Nucleic acid molecules as above which comprise gag, pol and env genes and which comprise adenine-thymidine-guanidine as the gag gene start codon are also particularly provided. Those which comprise gag, pol and env genes, the adenine-thymidine-guanidine as the gag gene start codon, and which further comprises SEQ ID NO 4 are also provided.

[0135] Included within the scope of the present invention, with particular regard to the nucleic acids above, are allelic variants, degenerate sequences and homologues. The present invention also includes variants due to laboratory manipulation, such as, but not limited to, variants produced during polymerase chain reaction amplification or site directed mutagenesis. It is also well known that there is a substantial amount of redundancy in the various codons which code for specific amino acids. Therefore, this invention is also directed to those nucleic acid sequences which contain alternative codons which code for the eventual translation of the identical amino acid. Also included within the scope of this invention are mutations either in the nucleic acid sequence or the translated protein which do not substantially alter the ultimate physical properties of the expressed protein. For example, substitution of valine for leucine, arginine for lysine, or asparagine for glutamine may not cause a change in functionality of the polypeptide. Lastly, a nucleic acid sequence homologous to the exemplified nucleic acid molecules (or allelic variants or degenerates thereof) will have at least 85%, preferably 90%, and most preferably 95% sequence identity with a nucleic acid molecule in the sequence listing.

[0136] It is known in the art that there are commercially available computer programs for determining the degree of similarity between two nucleic acid sequences. These computer programs include various known methods to determine the percentage identity and the number and length of gaps between hybrid nucleic acid molecules. Preferred methods to determine the percent identity among amino acid sequences and also among nucleic acid sequences include analysis using one or more of the commercially available computer programs designed to compare and analyze nucleic acid or amino acid sequences. These computer programs include, but are not limited to, GCG™ (available from Genetics Computer Group, Madison, Wis.), DNAsis™ (available from Hitachi Software, San Bruno, Calif.) and MacVector™ (available from the Eastman Kodak Company, New Haven, Conn.). A preferred method to determine percent identity among amino acid sequences and also among nucleic acid sequences includes using the Compare function by maximum matching within the program DNAsis Version 2.1 using default parameters.

[0137] Knowing the nucleic acid sequences of the present invention allows one skilled in the art to, for example, (a) make copies of those nucleic acid molecules, (b) obtain nucleic acid molecules including at least a portion of such nucleic acid molecules (e.g., nucleic acid molecules including full-length genes, full-length coding regions, regulatory control sequences, truncated coding regions), and (c) obtain similar nucleic acid molecules from other species. Such nucleic acid molecules can be obtained in a variety of ways including screening appropriate expression libraries with antibodies of the present invention; traditional cloning techniques using oligonucleotide probes of the present invention to screen appropriate libraries of DNA; and PCR amplification of appropriate libraries or DNA using oligonucleotide primers of the present invention. Preferred libraries to screen or from which to amplify nucleic acid molecules include canine cDNA libraries as well as genomic DNA libraries. Similarly, preferred DNA sources to screen or from which to amplify nucleic acid molecules include adult cDNA and genomic DNA. Techniques to clone and amplify genes are disclosed, for example, in Sambrook et al., ibid.

[0138] Recombination constructs can be made using the starting materials above or with additional materials, using methods well-known in the art. In general, the sequences can be manipulated to have ligase-compatible ends, and incubated with ligase to generate full constructs. For example, restriction enzymes can be chosen on the basis of their ability to cut at an acceptable site in both sequence to be ligated, or a linker may be added to convert the sequence end(s) to ones that are compatible. The methods for conducting these types of molecular manipulations are well-known in the art, and are described in detail in Sambrook et al., Molecular Cloning. A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989) and Ausubel et al., Current Protocols in Molecular Biology (Greene Publishing Associates, Inc., 1993). The methods described herein according to Tinland et al., 91 Proc. Natl. Acad. Sci.USA 8000 (1994) can also be used.

[0139] The present invention also includes nucleic acid molecules that are oligonucleotides capable of hybridizing, under stringent hybridization conditions, with complementary regions of other, preferably longer, nucleic acid molecules of the present invention. Oligonucleotides of the present invention can be RNA, DNA, or derivatives of either. The minimum size of such oligonucleotides is the size required for formation of a stable hybrid between an oligonucleotide and a complementary sequence on a nucleic acid molecule of the present invention. Minimal size characteristics are disclosed herein. The present invention includes oligonucleotides that can be used as, for example, probes to identify nucleic acid molecules, primers to produce nucleic acid molecules or therapeutic reagents. Stringent hybridization conditions are determined based on defined physical properties of the gene to which the nucleic acid molecule is being hybridized, and can be defined mathematically. Stringent hybridization conditions are those experimental parameters that allow an individual skilled in the art to identify significant similarities between heterologous nucleic acid molecules. These conditions are well known to those skilled in the art. See, for example, Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press, and Meinkoth, et al., 1984, Anal. Biochem. 138, 267-284.

[0140] Recombinant molecules of the present invention may also (a) contain secretory signals (i.e., signal segment nucleic acid sequences) to enable an expressed protein of the present invention to be secreted from the cell that produces the protein and/or (b) contain fusion sequences which lead to the expression of nucleic acid molecules of the present invention as fusion proteins. Recombinant molecules may also include intervening and/or untranslated sequences surrounding and/or within the nucleic acid sequences of nucleic acid molecules of the present invention.

[0141] One embodiment of the present invention includes recombinant vectors, which include at least one isolated nucleic acid molecule of the present invention, inserted into any vector capable of delivering the nucleic acid molecule into a host cell. Such a vector contains heterologous nucleic acid sequences, that is nucleic acid sequences that are not naturally found adjacent to nucleic acid molecules of the present invention and that preferably are derived from a species other than the species from which the nucleic acid molecule(s) are derived. The vector can be either RNA or DNA, either prokaryotic or eukaryotic, and typically is a virus or a plasmid. Recombinant vectors can be used in the cloning, sequencing, and/or otherwise manipulation of nucleic acid molecules of the present invention.

[0142] One type of recombinant vector, referred to herein as a recombinant molecule, comprises a nucleic acid molecule of the present invention operatively linked to an expression vector. The phrase operatively linked refers to insertion of a nucleic acid molecule into an expression vector in a manner such that the molecule is able to be expressed when transformed into a host cell. As used herein, an expression vector is a DNA or RNA vector that is capable of transforming a host cell and of effecting expression of a specified nucleic acid molecule. Expression vectors can be either prokaryotic or eukaryotic, and are typically viruses or plasmids. Expression vectors of the present invention include any vectors that function (i.e., direct gene expression) in recombinant cells of the present invention, including in bacterial, fungal, endoparasite, insect, other animal, and plant cells.

[0143] In particular, expression vectors of the present invention contain regulatory sequences such as transcription control sequences, translation control sequences, origins of replication, and other regulatory sequences that are compatible with the recombinant cell and that control the expression of nucleic acid molecules of the present invention. In particular, recombinant molecules of the present invention include transcription control sequences. Transcription control sequences are sequences which control the initiation, elongation, and termination of transcription. Particularly important transcription control sequences are those which control transcription initiation, such as promoter, enhancer, operator and repressor sequences. Suitable transcription control sequences include any transcription control sequences that can function in at least one of the recombinant cells of the present invention. A variety of such transcription control sequences are known to those skilled in the art. Preferred transcription control sequences include those which function in bacterial, yeast, insect and mammalian cells, such as, but not limited to, tac, lac, trp, trc, oxy-pro, omp/lpp, rrnB, bacteriophage lambda (such as lambda pL and lambda pR and fusions that include such promoters), bacteriophage T7, T71ac, bacteriophage T3, bacteriophage SP6, bacteriophage SP01, metallothionein, alpha-mating factor, Pichia alcohol oxidase, alphavirus subgenomic promoters (such as Sindbis virus subgenomic promoters), antibiotic resistance gene, baculovirus, Heliothis zea insect virus, vaccinia virus, herpesvirus, raccoon poxvirus, other poxvirus, adenovirus, cytomegalovirus (such as intermediate early promoters), simian virus 40, retrovirus, actin, retroviral long terminal repeat, Rous sarcoma virus, heat shock, phosphate and nitrate transcription control sequences as well as other sequences capable of controlling gene expression in prokaryotic or eukaryotic cells. Additional suitable transcription control sequences include tissue-specific promoters and enhancers as well as lymphokine-inducible promoters (e.g., promoters inducible by interferons or interleukins). Transcription control sequences of the present invention can also include naturally occurring transcription control sequences naturally associated with plants. The present invention also comprises expression vectors comprising a nucleic acid molecule described herein.

[0144] For instance, the following promoters would be useful in early expression of the present sequences: Ogs4B (Tsuchiya et al., 36 Plant Cell Physiology 487 (1994); TA29 (Koltunow et al., 2 Plant Cell 1201 (1990); A3 & A9 (Paul et al., 19 Plant Molecular Biology 611 (1992). In order to then constitutively express the sequences described above, the construct optionally contains, for example, a 35S promoter.

[0145] Vectors which comprise the above sequences are within the scope of the present invention, as are plants transformed with the above sequences. Vectors may be obtained from various commercial sources, including Clontech Laboratories, Inc. (Palo Alto, Calif.), Stratagene (La Jolla, Calif.), Invitrogen (Carlsbad, Calif.), New England Biolabs (Beverly, Mass.) and Promega (Madison, Wis.). Preferred vectors are those which are capable of transferring the sequences disclosed herein into plant cells or plant parts.

[0146] Recombinant DNA technologies can be used to improve expression of transformed nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within a host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications. Recombinant techniques useful for increasing the expression of nucleic acid molecules of the present invention include, but are not limited to, operatively linking nucleic acid molecules to high-copy number plasmids, integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites, Shine-Dalgarno sequences), modification of nucleic acid molecules of the present invention to correspond to the codon usage of the host cell, deletion of sequences that destabilize transcripts, and use of control signals that temporally separate recombinant cell growth from recombinant enzyme production during fermentation. The activity of an expressed recombinant protein of the present invention may be improved by fragmenting, modifying, or derivatizing nucleic acid molecules encoding such a protein.

[0147] Nucleic acids of the present invention may be transferred to cells according to the methods of the present invention, as well as using any of the following well-known means: infective, vector-containing bacterial strains (such as Agrobacterium rhizogenes and Agrobacterium tumefaciens) according to ie. Zambryski, 43 Ann. Rev. Pl. Physiol. Pl. Mol. Biol. 465 (1992); pollen-tube transformation [Zhon-xun et al., 6 Plant Molec. Bio. 165 (1988)]; direct transformation of germinating seeds [Toepfer et al., 1 Plant Cell 133 (1989)]; polyethylene glycol or electroporation transformation [Christou et al., 84 Proc. Nat. Acad. Sci. 3662 (1987)]; and biolistic processes [Yang & Cristou, Particle Bombardment Technology for Gene Transfer (1994)].

[0148] The transformed cells may be induced to form transformed plants via organogenesis or embryogenesis, according to the procedures of Dixon Plant Cell Culture: A Practical Approach (IRL Press, Oxford 1987).

[0149] Any seed, embryo, plant or plant part is amenable to the present techniques. Of course, the agronomically-significant seeds, embryos, plants or plant parts are preferred. Soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper; melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber, pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower; peanut; and olive are among the preferred seeds, embryos; plants or plant parts. Particularly preferred are: soybean, tobacco and maize seeds, embryos, plants or plant parts. However, Arabidopsis seeds, embryos, plants or plant parts are also preferred, since it is an excellent system for study of plant genetics.

[0150] Preferred are those genes or sequences which are agronomically significant For example, genes encoding male sterility, foreign organism resistance (viruses or bacteria), including genes which produce bacterial endotoxins, such as bacillus thurigiensis endotoxin, genes involved in specific biosynthetic pathways (eg. in fruit ripening, oil or pigment biosynthesis, seed formation, or carbohydrate metabolism), genes involved in environmental tolerance (eg. salt tolerance, lodging tolerance, cold/frost tolerance, drought tolerance, or tolerance to anaerobic conditions), or genes involved in nutrient content (eg. protein content, carbohydrate content, amino acid content, fatty acid content), genes involved in photosynthetic pathways, or genes involved in self-incompatibility. The choice of gene or sequence induced to recombine in the present invention is not limited. Examples of genes and how to obtain them are available through reference articles, books and supply catalogs, such as The Sourcebook (1-800-551-5291). Sambrook et al., Molecular Cloning. A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989) and Weising et al., 22 Ann Rev. Gen. 421 (1988) contain a synthesis of the information that is well-known in this art.

[0151] Plant envelope sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant envelope sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0152] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0153] (b) a nucleic acid sequence which encodes SEQ ID NO 5;

[0154] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0155] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 6;

[0156] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 6; and

[0157] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0158] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant envelope proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant envelope protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0159] Plant integrase sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant integrase sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0160] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0161] (b) a nucleic acid sequence which encodes SEQ ID NO 9;

[0162] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0163] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 10;

[0164] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 10; and

[0165] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0166] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant integrase proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant integrase protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0167] Plant reverse transcriptase sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant reverse transcriptase sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0168] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0169] (b) a nucleic acid sequence which encodes SEQ ID NO 11;

[0170] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0171] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 12;

[0172] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 12; and

[0173] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0174] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant reverse transcriptase proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant reverse transcriptase protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0175] Plant RNAseH sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant RNAseH sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0176] (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0177] (b) a nucleic acid sequence which encodes SEQ ID NO 15;

[0178] (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 95% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0179] (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 16;

[0180] (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 16; and

[0181] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0182] Plant cells comprising an isolated nucleic acid molecule above are particularly preferred. Also preferred are plant RNAseH proteins comprising an amino acid sequence encoded by the above. Methods to impart agronomically-significant characteristics to at least one plant cell are also provided, comprising: contacting a plant RNAseH protein as described to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.

[0183] Plant retroelement sequences and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, wherein said nucleic acid molecules encode at least a portion of a plant retroelement sequence and comprises a nucleic acid sequence selected from the group consisting of:

[0184] (a) a nucleic acid sequence which has more than 95% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0185] (b) a nucleic acid sequence which is selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO 17;

[0186] (c) a nucleic acid sequence which encodes an amino acid sequence which has more than 90% identity to an amino acid sequence selected from the group consisting of SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; SEQ ID NO 18, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0187] (d) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18;

[0188] (e) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; and

[0189] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).

[0190] Nucleic acid molecule as above, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those nucleic acid molecules as described wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content. Also more preferred are those isolated nucleic acid molecule as described, wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0191] Seeds and plants comprising a nucleic acid molecule as described are also preferred. More preferred are plants as described, wherein the plant is selected from the group consisting of: soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper; melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber, pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower; peanut; and olive. Most preferred are plants as described which is a soybean plant.

[0192] Plant retroelements comprising an amino acid sequence encoded by a nucleic acid sequence described are also provided. Plant cells comprising a nucleic acid molecule described herein, as well as plant retroviral proteins encoded by nucleic acid molecules described herein are provided.

[0193] Moreover, methods to transfer nucleic acid into a plant cell, comprising contacting a nucleic acid molecule of the present invention with at least one plant cell under conditions sufficient to allow said nucleic acid molecule to enter at least one cell of said plant are provided. In particular there is provided, methods to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroelement of the present invention to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic. Methods as described, wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content are preferred, as are methods wherein the agronomically-significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content

[0194] Plant retroelement sequences comprising specialized signals, and constructs which comprise the sequences are provided, as are cells, seeds, embryos and plants comprising them. Preferred are isolated nucleic acid molecules, comprising a nucleic acid sequence selected from the group consisting of:

[0195] (a) a nucleic acid sequence which has more than 95% identity to SEQ ID NO 2; wherein said identity can be determined using the DNAsis computer program and default parameters;

[0196] (b) a nucleic acid sequence which is SEQ ID NO 2;

[0197] (c) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 4; and

[0198] (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).

[0199] Plant retroelements as described above, which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those methods wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content or those wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0200] Preferred are plant retroviral particles comprising an isolated retroelement as described, and seeds and plants comprising the retroelements as described. More preferred plants include soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper; melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber; pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower, peanut; and olive. Soybean is most preferred.

[0201] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroelement as described with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell. Methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroelement as described with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell are also preferred. Those methods wherein the plant retroelement is contacted with said cell via a plant retroviral particle described herein are preferred.

[0202] Plant retroviruses are also provided. In particular, plant retroviral particles comprising a plant-derived retrovirus envelope protein are provided. Plant retroviral particles comprising a plant-derived retrovirus envelope protein and which further comprise a plant retroviral protein selected from the group consisting of: plant-derived integrase; plant derived reverse transcriptase; plant-derived gag; and plant-derived RNAseH are preferred.

[0203] Plant retroviral particles comprising specialized retroviral proteins, and cells, seeds, embryos and plants which comprise the retroviral particles are provided. Preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0204] (a) a nucleic acid sequence comprising (i) a nucleic acid sequence which encodes at least one plant retroviral envelope protein, and (ii) a nucleic acid sequence which has more than 60% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9, SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0205] (b) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence (a);

[0206] (c) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid sequence of (a); and

[0207] (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).

[0208] In particular, there are provided plant retroviral particles, wherein said nucleic acid sequence as described in (a) comprises a plant envelope nucleic acid specifically mentioned in claim 6 is preferred. Those particles which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred.

[0209] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0210] More preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0211] (a) a nucleic acid sequence which has more than 80% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0212] (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15;

[0213] (c) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b);

[0214] (d) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); and

[0215] (e) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); and a nucleic acid sequence of (d).

[0216] Nucleic acids as above, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic are preferred. More preferred are those nucleic acids wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content, or wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.

[0217] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0218] Also preferred are isolated retroviral particles comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of:

[0219] (a) a nucleic acid sequence which has more than 60% identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0220] (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31;

[0221] (c) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b);

[0222] (d) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); and

[0223] (e) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); and a nucleic acid sequence of (d).

[0224] Also preferred are isolated retroviral particles comprising a plant retroviral sequence encoded by a nucleic acid sequence selected from the group consisting of:

[0225] (a) a nucleic acid sequence which has more than 80% identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO 1; SEQ ID NO 2; SEQ ID NO 3, wherein said identity can be determined using the DNAsis computer program and default parameters;

[0226] (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 1; SEQ ID NO 2; and SEQ ID NO 3;

[0227] (c) a nucleic acid sequence which encodes SEQ ID NO 4;

[0228] (d) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c);

[0229] (e) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c) and

[0230] (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (e); and a nucleic acid sequence of (f).

[0231] Plant retroviral particles as described above, which further comprises an envelope-encoding nucleic acid sequence specifically described herein are preferred. Preferred are those retroviral particles which further comprise at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic.

[0232] Also provided are methods to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle as described above to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell. More preferred are methods to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle as described to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.

[0233] Also provided, as part of the present invention, are isolated nucleic acid having at least 20 contiguous nucleotides of the sequence shown in SEQ ID NO 17. “At least” means that this is the lower limit and the number can be any whole number increment up to the total number of bases in SEQ ID NO 17. For example, isolated nucleic acid sequences which are 25, 30, 35, 40, 45, 50, 55, 60, 65 and 70 are within the scope of the present invention.

[0234] The following paragraph is designed to elaborate on the best mode and is not indicative of the sole means for making and carrying out the present invention. This paragraph is not intended to be limiting. The best way to make the present nucleic acids is to clone the nucleic acids from the respective organisms or amplified from genomic cDNA by the polymerase chain reaction using appropriate primers. The best way to make the present retroelements is to assemble the nucleic acids using standard cloning procedures. Transcriptional controls can be manipulated by inserting enhancers in or near the 5′ LTR. Marker genes or genes of interest can be inserted within the retroelement. The best way to make the present retroviral particles is to express the retroelement, preferrably at high levels, in plant cells and the particles harvested by sucrose gradient fractionation. The best way to use the present nucleic acids is by allowing retroviral particles to come into contact with plant cells. Expression of marker genes carried by the retroelement can be used as one measure of infection and integration.

[0235] The following examples are not intended to limit the scope of the present invention as described and claimed. They are simply for the purpose of illustration.

EXAMPLES Example 1 Characterizing the Arabidopsis Retroelements (“Tat” and“Athila” Elements)

[0236] Plant material and Southern hybridizations: The Arabidopsis Information Service supplied the following seed stocks (Kranz and Kirchheim (1987) Arabidopsis Inform. Serv. 24): Col-0, La-0, Kas-1, Co4, Sei-0, Mv-0, Ll-0, Cvi-0, Fi-3, Ba-1, Hau-0, Aa-0, Ms-0, Ag-0, Ge-0, No-0 and Mh-0. Genomic DNA was extracted using Qiagen genomic tips and protocols supplied by Qiagen. For Southern hybridizations, the resulting DNA was digested with EcoRI, electrophoresed on 0.8% agarose and transferred to Gene Screen Plus membranes using the manufacturer's alkaline transfer protocol (New England Nuclear). All hybridizations were performed as described. Church and Gilbert (1984) Proc. Natl. Acad. Sci. USA 81: 1991-1995.

[0237] Library screening, probe preparation and PCR: Tat1 clones were obtained by screening a Landsberg erecta (La-0) 1 phage library (Voytas et al. (1990) Genetics 126: 713-721), using a probe derived by PCR amplification of La-0 DNA. The primers for probe amplification were based on the three published Tat1 sequences (DVO158, 5′-GGGATCCGCAATTAGAATCT-3′; DVO159, 5′-CGAATTCGGTCCACTTCGGA-3′). Peleman et al. (1991) Proc. Natl. Acad. Sci. USA 88: 3618-3622. Subsequent probes were restriction fragments of cloned Tat1 elements, and all probes were radiolabeled by random priming (Promega). Long PCR was performed using the Expand Long Template PCR System (Boehringer Mannheim) with LTR-specific primers (DVO354, 5′-CCACAAGATTCTAATTGCGGATTC-3′; DVO355, 5 ′-CCGAAATGGACCGAACCCGACATC-3′). The protocol used was for PCR amplification of DNA up to 15 kb. The following PCR primers were used to confirm the structure of Tat1-3: DVO405 (5′-TTTCCAGGCTCTTGACGAGATTFG-3′) for the 3′ non-coding region, DVO385 (5′-CGACTCGAGCTCCATAGCGATG-3′) for the second ORF of Tat1-3 (note that the seventh base was changed from an A to a G to make an XhoI and a SalI restriction site) and DVO371 (5′-CGGATTGGGCCGAAATGGACCGAA-3′) for the 3′ LTR.

[0238] DNA sequencing: Clones were sequenced either by the DNA sequencing facility at Iowa State University or with the fmol sequencing kit (Promega). DNA from the 1 phage clones was initially subcloned into the vector pBluescript II KS-and transformed into the E. coli host strain XL1 Blue (Stratagene). AUSUBEL et al. (1987) Current Protocols in Molecular Biology. Greene/Wiley Interscience, New York. Subclones in the vector pMOB were used for transposon mutagenesis with the TN 1000 sequencing kit (Gold Biotechnologies). Transposon-specific primers were used for DNA sequencing reactions.

[0239] Sequence analysis: Sequence analysis was performed using the GCG software package (Devereux et al. (1984) Nucl. Acids Res. 12: 387-395), DNA Strider 1.2 (Marck (1991) DNA Strider 1.2, Gif-sur-Yvette, France), the BLAST search tool (Altschul et al. (1990) J. Mol. Biol. 215: 403-410) and the tRNAscan-SE 1.1 program (Lowe and Eddy (1997) Nucl. Acids Res. 25: 955-964). Phylogenetic relationships were determined by the neighbor-joining distance algorithm using Phylip (Felsenstein (1993) PHYLIP (Phylogeny Inference Package). Department of Genetics, University of Washington, Seattle; SAITOU and NEI (1987) Mol. Biol. Evol. 4: 406-425) and were based on reverse transcriptase amino acid sequences that had been aligned with ClustalW1.7. THOMPSON, et al. (1994) Nucl. Acids Res. 22: 4673-4680. Transmembrane helices were identified using the PHDhtm program. ROST et al. (1995) Prot. Science 4: 521-533. All DNA sequences have been submitted to the DDBS/EMBL/GenBank databases under the accession numbers X12345, X23456, X34567 and X45678.

[0240] Results

[0241] Tat1 is a retrotransposon: Tat1 insertions share features with retrotransposon solo LTRs. We reasoned that if Tat1 is a retrotransposon, then there should be full-length elements in the genome consisting of two Tat1 sequences flanking an internal retrotransposon coding region. To test this hypothesis, additional Tat1 elements were isolated by screening a Landsberg (La-0) genomic DNA library with a Tat1 probe. Twenty-one 1 phage clones were isolated and Southern analysis revealed two clones (pDW42 and pDW99) each with two copies of Tat1 (data not shown). The two Tat1 elements in each clone were sequenced, along with the intervening DNA. All Tat1 sequences shared >89% nucleotide identity to the previously characterized Tat1a-Tat1c elements. Peleman et al. (1991) Proc. Natl. Acad. Sci. USA 88: 3618-3622. In clone pDW99, the 5′ and 3′ Tat1 sequences were 433 bases in length and only differed at two base positions. These Tat1 sequences also had conserved features of LTRs, including the dinucleotide end-sequences (5′ TG-CA 3′) that were part of 12 base inverted terminal repeats. If the two Tat1 elements in clone pDW99 were retrotransposon LTRs, then both, along with the intervening DNA, should be flanked by a target site duplication. A putative five base target site duplication (TATGT) was present immediately adjacent to the 5′ and 3′ Tat1 elements, supporting the hypothesis that they and the intervening DNA inserted as a single unit. In clone pDW42, the 5′ Tat1 was 432 bases in length and shared 98% nucleotide sequence identity to the 3′ Tat1. The last ˜74 bases of the 3′ Tat1 was truncated during library construction and lies adjacent to one phage arm. A target site duplication, therefore, could not be identified in this clone.

[0242] DNA sequences were analyzed for potential coding information between the 5′ and 3′ Tat1 elements. Nearly identical ORFs of 424 and 405 amino acids were found encoded between the Tat1 sequences in pDW42 and pDW99, respectively. The derived amino acid sequences of these ORFs were used to search the DNA sequence database with the BLAST search tool, and significant similarity was found to the Zea mays retrotransposable element Zeon-1 (p=4.4e−08). HU et al. (1995) Mol. Gen. Genet. 248: 471-480. The ORFs have ˜44% similarity across their entirety to the 628 amino acid ORF encoded by Zeon-1 (see below). The Zeon-1 ORF includes a zinc finger motif characteristic of retrotransposon gag protein RNA binding domains. Hu et al. (1995) Mol. Gen. Genet. 248: 471-480. Although the Tat1 ORFs do not include the zinc finger motif, the degree of similarity suggests that they are part of a related gag protein.

[0243] If the Tat1 sequences in pDW42 and pDW99 defined retrotransposon insertions, a PBS would be predicted to lie adjacent to the 5′ Tat1 elements in both clones. The putative Tat1 PBS shares similarity with PBSs of Zeon-1 and another maize retrotransposon called Cinful (see below), but it is not complementary to an initiator methionine tRNA as is the case for most plant retrotransposons. Additionally, a possible polypurine tract (PPT), the primer for second strand cDNA synthesis, was observed one base upstream of the 3′ Tat1 sequence in both phage clones (5′-GAGGACTTGGGGGGCAAA-3′). We concluded from the available evidence that Tat1 is a retrotransposon, and we have designated the 3960 base insertion in pDW42 as Tat1-1 and the 3879 base insertion in pDW99 as Tat1-2. It is apparent that both Tat1-1 and Tat1-2 are non-functional. Their ORFs are truncated with respect to the coding information found in transposition-competent retrotransposons, and they lack obvious pol motifs.

[0244] In light of our findings, the previously reported Tat1 sequences can be reinterpreted. Tat1a and Tat1b, which are flanked by putative target site duplications, are solo LTRs. Tat1c, the only element without a target site duplication, is actually the 5′ LTR and part of the coding sequence for a larger Tat1 element.

[0245] Copy number of Tat1 among A. thaliana ecotypes: To estimate Tat1 copy number, the 5′ LTR, gag and the 3′ non-coding region were used as separate probes in Southern hybridizations. The Southern filters contained genomic DNA from 17 ecotypes representing wild populations of A. thaliana from around the world. This collection of ecotypes had previously been used to evaluate retrotransposon population dynamics. Konieczny et al. (1991) Genetics 127: 801-809; Voytas et al. (1990) Genetics 126: 713-721; Wright et al. (1996) Genetics 142: 569-578. Based on the hybridization with the gag probe, element copy number ranges from two to approximately ten copies per ecotype. The copy number of the LTRs is higher, likely due to the presence of two LTRs flanking full-length elements or solo LTRs scattered throughout the genome. The Tat1 copy number contrasts with the copy numbers (typically less than three per ecotype) observed for 28 other A. thaliana retrotransposon families. Konieczny et al. (1991) Genetics 127: 801-809; Voytas et al. (1990) Genetics 126: 713-721; Wright et al. (1996) Genetics 142: 569-578. In addition, the Tat1-hybridizing restriction fragments are highly polymorphic among strains. This degree of polymorphism, coupled with the high copy number, suggested that Tat1 has been active in transposition since the separation of the ecotypes.

[0246] The Tat1 3′ non-coding region contains DNA sequences from elsewhere in the genome: In an attempt to identify a complete and functional Tat1 element, LTR-specific primers were used in PCR reactions optimized for amplification of large DNA fragments. Most full-length retrotransposable elements are between five and six kb in length. DNAs from all 17 ecotypes were used as templates, and each gave amplification products of ˜3.2 kb, the size predicted for Tat1-1 and Tat1-2 (data not shown). In La-0, however, a 3.8 kb PCR product was also recovered. This PCR product was cloned, sequenced and called Tat1-3. This insertion is expected to be about 4.6 kb in total length if the LTR sequences are included.

[0247] Tat1-3 differed from Tat1-1 and Tat1-2 in that it had two ORFs separated by stop codons and a 477 base insertion in the 3′ non-coding region. The first ORF (365 amino acids) was similar to but shorter than the ORFs of the other Tat1 elements. The sequences constituting the second ORF (188 amino acids) were not present in the other Tat1 insertions and were not related to other sequences in the DNA databases. Database searches with the 477 base insertion in the 3′ non-coding region, however, revealed three regions of similarity to other genomic sequences. A region of 113 bases matched a region of 26 bp repeats in the 5′ untranslated sequence of the AT-P5C1 mRNA, which encodes pyrroline-5-carboxylate reductase (p=2.1e−19). Verbruggen et al. (1993) Plant Physiol. 103: 771-781. In addition, 50 bases appear to be a remnant of another retrotransposon related to Tat1. These 50 bases are 71% identical to the 3′ end of the Tat1-3 LTR and the putative primer binding site. The putative primer binding site, however, is more closely related to those of other plant retrotransposons such as Huck-2 (Sanmiguel et al. (1996) Science 274: 765-768). Finally, sequences in the remainder of the insertion showed significant similarity to a region on chromosome 5. To confirm that Tat1-3 was not a PCR artifact, two additional primer pairs were used in separate amplifications. Both amplifications gave PCR products of the predicted sizes, which were cloned and confirmed to be Tat1-3 by DNA sequencing.

[0248] PCR amplifications with the additional primer pairs also yielded a product 0.8 kb longer than that expected for Tat1-3. This product was cloned, sequenced and found to be another Tat1 element, designated Tat1-4. This element has sequences similar to a Tat1 LTR, polypurine tract and the second ORF of Tat1-3. In Tat1-4, 1182 bases of DNA are found in the 3′ non-coding region at the position corresponding to the 477 base insertion in Tat1-3. This region does not match any sequences in the DNA databases.

[0249] Other Tat1-like elements in A. thaliana : A BLAST search of DNA sequences generated by the A. thaliana genome project identified two more solo LTRs similar to Tat1. All share similarities throughout, but most strikingly, they are very well conserved at the 5′ and 3′ ends where it is expected integrase would bind. Braiterman and Boeke (1994) Mol. Cell. Biol. 14: 5731-5740. These conserved end-sequences suggest that the integrases encoded by full-length elements are also related, and that the LTRs have evolved under functional constraints; that is, they are not simply degenerate Tat1 LTRs. The two new LTRs are designated as Tat2-1 and Tat3-1. Tat2-1 is 418 bases long, is flanked by a five base target site duplication (CTATT) and is ˜63% identical to the Tat1-2 5′ LTR. Tat3-1 is 463 bases long and is also flanked by a target site duplication (ATATT). Tat3-1 is ˜53% identical to the Tat1-2 5′ LTR.

[0250] Tat1 and Athila are related to Ty3/gypsy retrotransposons: Further analysis of data from the A. thaliana genome project revealed two slightly degenerate retrotransposons with similarity to the Tat1 ORF. These elements were identified within the sequence of the P1 phage clones MXA21 (Accession AB005247; bases 54,977-66,874) and MX110 (Accession AB005248; bases 24,125-35,848). Each has two LTRs, a putative PBS, and long ORFs between their LTRs. The genetic organization of these elements is depicted in FIGS. 5A and 6A. Amino acid sequence analysis indicated the presence of an RNA binding domain that defines gag in both elements. This region is followed by conserved reverse transcriptase, RNaseH, and integrase amino acid sequence domains characteristic of pol (data not shown). Classification of eukaryotic retrotransposons into the Ty1/copia elements (Pseudoviridae) and Ty3/gypsy elements (Metaviridae) is based on pol gene structure. Boeke et al. (1998) Metaviridae. In Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Springer-Verlag, New York.; Boeke et al. (1998b) Pseudoviridae. In Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Springer Verlag, New York. The domain order of the pol genes (reverse transcriptase precedes integrase ) and similarities among their encoded reverse transcriptases (see below) identifies these elements as the first full-length A. thaliana Ty3/gypsy elements.

[0251] Because the characterized Tat1 insertions do not encode pol genes, this element family could not be classified. However, the amino acid sequence of the Tat1-2 ORF is 51% similar to the gag region of the MXA21 retrotransposon. Since plant retrotransposons within the Ty1/copia or Ty3/gypsy families, even those with highly similar pol genes, share little amino acid sequence similarity in their gag regions, Tat1 is likely a Ty3/gypsy element. This conclusion is further supported by the report that the Tat-like Zeon-1 retrotransposon is very similar to a Z. mays Ty3/gypsy element called cinful (Bennetzen (1996) Trends Microbiol. 4: 347-353); however, only the 5′ LTR and putative primer binding site (PBS) sequences are available in the sequence database for analysis (Accession U68402). Because of the extent of similarity to Tat1, we have named the MXA21 insertion Tat4-1.

[0252] The gag region of the MX110 element is 62% similar (p=1.1e−193) to the first ORF of Athila, which has previously been unclassified (Pelissier et al. (1995) Plant Mol. Biol. 29: 441 452). This implies that Athila is also a Ty3/gypsy element, and we have designated the MX110 insertion as Athila1-1. Our classification of Athila as a Ty3/gypsy element is further supported by the observation that the Athila gag amino acid sequences shares significant similarity to the gag protein encoded by the cyclops-2 Ty3/gypsy retrotransposon of pea (Accession AJ000640; p=1.1e−46; data not shown). Further analysis of the available A. thaliana genome sequences identified three additional Athila homologs. They include an additional Athila1 element, designated Athila1-2, and two more distantly related Athila-like elements, designated Athila2-1 and Athila3-1.

[0253] In addition to similarities among their gag amino acid sequences, the Tat elements have short LTRs (<550 bp) and long 3′ non-coding regions (>2 kb). In contrast, the Athila-like elements have long LTRs (>1.2 kb) and are very large retrotransposons (>11 kb). One additional feature to note about both the Athila-like and Tat-like elements is the high degree of sequence degeneracy of their internal coding regions. This contrasts with the near sequence identity of their 5′ and 3′ LTRs, which is typically greater than 95%. Because a single template is used in the synthesis of both LTRs, LTR sequences are usually identical at the time of integration. The degree of sequence similarity between the LTRs suggests that most elements integrated relatively recently. The polymorphisms observed in the internal domains of these insertions, therefore, may have been present in their progenitors, and these elements may have been replicated in trans.

[0254] A novel, conserved coding region in Athila elements: A surprising feature of Athila1-1 is the presence of an additional ORF after integrase. Like gag, this ORF shares significant similarity across its entirety (p=3.8e−08) to the second ORF of Athila. This ORF is also encoded by the Athila2-1 and Athila3-1 elements, although it is somewhat more degenerate. The presence of this coding sequence among these divergent retrotransposons suggests that it plays a functional role in the element replication cycle. However, the ORF shows no similarity to retrotransposon gag or pol genes. The retroviruses and some Ty3/gypsy retrotransposons encode an env gene after integrase. Although not well-conserved in primary sequence, both viral and retrotransposon envelope proteins share some structural similarities. They are typically translated from spliced mRNAs and the primary translation product encodes a signal peptide and a transmembrane domain near the C-terminus. All four families of Athila elements encode a domain near the center of the ORF that is strongly predicted to be a transmembrane region (70% -90% confidence, depending on the element analyzed) (ROST et al. (1995) Prot. Science 4: 521-533). Two retrotransposons, Athila and Athila2-1, also have a hydrophobic transmembrane domain near the 5′ end of their env-like ORFs, which may serve as a secretory signal sequence. Von Heijne (1986) Nucl. Acids Res. 14: 4683-4690.

[0255] Two lineages of plant Ty3/gypsy retrotransposons: Relationships among Ty3/gypsy retrotransposons from A. thaliana and other organisms were assessed by constructing a neighbor-joining tree of their reverse transcriptase amino acid sequences. Included in the analysis were reverse transcriptases from two additional families of A. thaliana Ty3/gypsy elements that we identified from the unannotated genome sequence data (designated Tma elements; Tma1-1 and Tma3-1); two other Tma element families were identified in the genome sequence that did not encode complete reverse transcriptases (Tma2-1 and Tma4-1; Table 1). Also included in the phylogenetic analyses were reverse transcriptases from a faba bean retrotransposon and the cyclops-2 element from pea. The plant Ty3/gypsy group retrotransposons resolved into two lineages: One was made up of del1 from lily, the IFG7 retrotransposon from pine, reina from Z. mays, and Tma1-1 and Tma3-1. This group of elements formed a single branch closely related to numerous fungal retrotransposons (branch 1). The second branch (branch 2) was well-separated from all other known Ty3/gypsy group elements, and was further resolved into two lineages: Athila1-1, cyclops-2 and the faba bean reverse transcriptase formed one lineage (the Athila branch), and Tat4-1 and Grandel-4 from Zea diploperennis formed a separate, distinct branch (the Tat branch).

[0256] Primer binding sites: Most plant Ty1/copia retrotransposons as well as the branch 1 Ty3/gypsy elements have PBSs complementary to the 3′-end of an initiator methionine tRNA. This is not the case for any of the branch 2 Ty3/gypsy elements. We compared the putative PBSs of Tat-branch and Athila-branch elements to known plant tRNA genes as well as to the 11 tRNA genes that had been identified to date in sequences generated by the A. thaliana genome project. In addition, we searched the unannotated A. thaliana genome sequences and identified 30 more A. thaliana tRNA genes using the program tRNAscan-SE (Lowe and Eddy (1997) Nucl. Acids Res. 25: 955-964). The PBS of Tat1 is complementary to 10 bases at the 3′ end of the asparagine tRNA for the AAC codon; these 10 bases are followed by a two base mismatch and six additional bases of perfect complementarity. The Tat4-1 PBS is complementary to 20 bases at the 3′ end of the arginine tRNA for the AGG codon with one mismatch 10 bases from the 3′ end; Huck-2, Grande-zm1, Grande1-4, and the retrotransposon-like insertion in the 3′ non-coding region of Tat1-3 all have 20-base perfect complementarity to this tRNA. The PBS of Athila1-1 is perfectly complementary to 15 bases at the 3′ end of the aspartic acid tRNA for the GAC codon, and Athila and Athila2-1 have 13 bases of complementarity to this tRNA. At this time there is no known plant tRNA complementary to the PBS of Zeon-1, which has the same PBS as the maize retrotransposon cinful. As more tRNA sequences become available, a candidate primer may be identified for these elements.

Example 2 Characterizing the Pisum sativum Retroelement (“Cyclops” Element) Env Gene

[0257] After identifying the retrovirus-like elements in A. thaliana , the element called Cyclops2 from Pisum sativum (Chavanne et al. (1998) Plant Mol. Biol. 37: 363-375) was examined. Comparison of this element to the Athila-like elements both in size and amino acid and nucleotide sequence composition was made. Cyclops2 also encodes an open reading frame (ORF) in the position corresponding to the env-like gene of the Athila elements. This Cyclops2 ORF was examined using the same methods used to characterize the Athila group env-like genes (see Example 1). The Cyclops2 ORF was found to have a potential splice site at its N-terminus and transmembrane domains at the N-terminus, the central region and the C-terminus. Based on the presence of these features, it was concluded that Cyclops2 is a retrovirus-like retroelement that encodes on env-like gene.

Example 3 Obtaining the Soybean Retroelements (“Calypso” Elements)

[0258] Materials and Methods

[0259] Library Screening and Southern Hybridization. A soybean genomic lambda phage library (line L85-3044) was initially screened with a reverse transcriptase probe under low stringency conditions (50 degrees Celsius with a 1% SDS wash) (Church and Gilbert (1984) Proc. Natl. Acad. Sci. USA 81: 1991-1995). The library was previously described (Chen et al. (1998) Soybean Genetics Newsletter 25: 132-134). The probe was obtained by PCR amplification of genomic P. sativum DNA using primers based on the reverse transcriptase of Cyclops2 ( DVO701 and DVO702). All probes were radio-labeled using random primers and protocols supplied by Promega (Madison, Wis.). For Southern hybridizations, DNA was digested, electrophoresed on 0.8% agarose gels, and transferred to Gene Screen Plus membranes using the manufacturerls alkaline transfer protocol (New England Nuclear, Boston, Mass.). All high stringency hybridizations were as described (Church and Gilbert (1984) Proc. Natl. Acad. Sci. USA 81: 1991-1995).

[0260] DNA sequencing. Lambda phage clones were subcloned into the vector pBluescript KSII—and transformed into the E.coli host strain XL1 Blue (Stratagene, La Jolla, Calif.) (Ausubel et al., Current Protocols in Molecular Biology (Greene Publishing Associates, Inc., 1993). Subclones were sequenced by primer walking at the Iowa State University DNA sequencing facility.

[0261] Sequence Analysis. DNA Sequence analysis was performed using the GCG software package (Devereux et al. (1984) Nucleic Acids Res. 12: 387-395), DNA Strider 1.2 (Marck (1991) DNA Strider 1.2, Gif-sur-Yvette, France) and the BLAST search tool (Altschul et al. (1990) J. Mol. Biol. 215: 403-410). Phylogenetic relationships were determined by the neighbor-joining distance algorithm (Saitou and Nei (1987) Mol. Biol. Evol. 4: 406-425) using PAUP v4.0 beta 1 (Swofford (1993) Illinois Natural History Survey, Champaign, Ill.) and were based on reverse transcriptase amino acid sequences that had been aligned with ClustalX v1.63b (Thompson et al. (1994) Nucl. Acids Res. 22: 4673-4680). Transmembrane helices were identified using the PHDhtm program and TMPred (Rost et al. (1995) Prot. Science 4: 521-533; Hofmann and Stoffel (1993) Biol. Chem. 374: 166).

[0262] Results

[0263] Retrovirus-like elements in Glycine max. Soybean retrovirus-like elements were identified by a low stringency (50 degrees C.) screen of a soybean lambda library using a reverse transcriptase probe. The probe was based on a sequence from Cyclops2 (Chavanne et al. (1998) Plant Mol. Biol. 37: 363-375). The screen produced 63 lambda clones that appeared to contain a retrovirus-like reverse transcriptase based on hybridization to the probe. Thirty-five of these putative elements were sequenced to varying degrees and 24 encoded readily identifiable retrovirus-like sequences. Most of the elements were distantly related and had premature stop codons, frame shifts, deletions or insertions. A related group of three elements and another related pair were completely sequenced and analyzed. The three elements in the first group are referred to as Calypso1-1, Calypso1-2, and Calypso1-3. The elements in the second pair are referred to as Calypso2-1 and Calypso2-2. The remaining soybean retrovirus-like elements will be given the Calypso name and a sequential designator number based on their family grouping.

[0264] The Calypso retrovirus-like elements have the same overall structure and sequence homology as the previously described Athila and Cyclops elements. The elements are ˜12 kb in length; they have a 5′ LTR, a PBS (Primer Binding Site), a gag protein, a pol protein, a spacer, an env-like protein, another spacer region, a PPT (Polypurine Tract) and a 3′ LTR. The LTRs vary from ˜1.3 to ˜1.5 kb in length and characteristically begin with TG and end with CA. The PBS is similar to that used by the Athila and Cyclops elements; it is 4 to 6 bases past the 5′ LTR and matches the 3′ end of a soybean aspartic acid tRNA for 18 to 19 bases with 1 mismatch. The fact that the sequences of the Calypso primer binding sites are shared with the A. thaliana and P. sativum retrovirus-like elements, indicates that this sequence is a unique marker for envelope-encoding retroelements. The gag protein extends ˜850 amino acids and encodes a zinc finger domain (characterized by the amino acid motif CxxCxxxHxxxxC) and a protease domain (characterized by the amino acid motif LIDLGA). These domains are located at approximately the same positions within gag as in other retroelements. The ˜600 amino acid reverse transcriptase region follows gag and has the conserved plant retrovirus-like motifs which approximate the following amino acids: KTAF, MP/SFGLCNA, V/I/MEVFMDDFS/WV/I, FELMCDASDYAI/VGAVLGQR, and YATT/IEKEL/MLAIVF/YAL/FEKFR/KSYLI/VGSR/KV, respectively. The ˜450 amino acid integrase domain has the plant retrovirus-like integrase motifs that approximate HCHxSxxGGH30xCDxCQR for the Zn finger as well as two other motifs that approximate WGIDFI/V/MGP, and PYHPQTxGQA/VE. After integrase, there is a ˜0.7 kb spacer then a ˜450 amino acid env-like protein coding region. The env-like protein of the Calypso elements is well conserved through most of the ORF but conservation decreases toward the C-terminus. The conservation includes 2 or 3 presumed transmembrane domains and a putative RNA splice site acceptor. The env-like protein is followed by a ˜2 kb spacer then a polypurine tract with the approximate sequence ATITGGGGG/AANNT. The 3′ LTR starts immediately after the final T of the PPT.

[0265] Calypso elements are abundant and heterogeneous. The Calypso elements appear to be abundant in the soybean genome. High stringency Southern blots of soybean DNA probed with reverse transcriptase, gag or env-like sequences produced smeared hybridization patterns, suggesting that the elements are abundant and heterogeneous. Their heterogeneity was also supported by DNA sequence analysis, which revealed a maximum of 93% nucleotide identity among elements, and most elements averaged ˜88% nucleotide identify. This identity can be region-specific or dispersed over the element's entirety. For example, reverse transcriptase, integrase and envelope-like coding regions may be well conserved, whereas the LTR, gag and spacer regions may have very little sequence conservation.

[0266] Phylogenetic analysis of Calypso reverse transcriptase. The reverse transcriptase of retroelements is the preferred protein for assessment of phylogenetic relationships (Xiong and Eickbush (1990) EMBO J. 9: 3353-3362). This is due to the high degree of amino acid sequence conservation found in reverse transcriptase proteins from many sources. The Calypso retrovirus-like elements were compared to previously described Ty3/gypsy and retrovirus-like elements from plants, fungi and invertebrate animals. The Calypso elements formed a distinct group with other plant retrovirus-like elements from A. thaliana and P. sativum and Faba bean. This group did not include plant Ty3/gypsy elements that are members of the metavirus genus. This indicates that the plant retrovirus-like elements from these four plant species are closely related and form a new element group that may be present in all or most plant species.

[0267] The Calypso reverse transcriptase and integrase are well-conserved. Frame shifts in the retrovirus-like elements were repaired through sequence comparison between the retrovirus-like elements from A. thaliana, P. sativum and G. max. Restoration typically involved an insertion or deletion of a single nucleotide or a single nucleotide substitution. When the edited ORFs of seven plant retrovirus-like elements from three species were compared, it was found that the gag domain had very little conservation. The amino acid sequence around the protease domain was reasonably conserved (˜50%) but the reverse transcriptase and integrase domains were highly conserved (˜70%).

[0268] The env-like ORF of Calypso is well-conserved. Animal retrovirus env proteins share little in common. They are however cleaved into two functional units that consist of the surface (SU) and transmembrane (TM) peptides. The SU peptide contains a transmembrane secretory signal at the N-terminus. The TM peptide has two transmembrane domains, one at the N-terminus, which functions in membrane fusion, and another near the C-terminus, which acts as an anchor site. The retrovirus env protein is expressed from an RNA that is spliced near the beginning of the env ORF. There are currently nine Athila group elements from A. thaliana that have an identifiable env-like ORF. Alignment of the env-like amino acid sequence shows that there are five subgroups of env-like proteins in the Athila family. Three are distinct, four are closely related and another pair is closely related. As a whole, these env-like sequences share limited homology over the entire length of the ORF, but within subgroups, they share high homology (data not shown). Some of the Athila env-like proteins have an apparent secretory peptide and a central transmembrane domain, suggesting that they may have an env-like function.

[0269] Among the Calypso elements, seven have been characterized that encode env-like ORFs. These env-like ORFs form four families that have a high degree of overall sequence similarity beginning at the first methionine and continuing for three quarters of the ORF; sequence similarity falls off dramatically near the C-terminus. The amino acid sequence at the first methionine has the consensus sequence QMASR/KKRR/KA, which appears to be a nuclear targeting signal, however, the program PSORT only predicts a 0.300 confidence level for this targeting role (Nakai and Horton (1999) Trends Biochem. Sci. 24: 34-36). A similar sequence (ASKKRK) is found at the same position in the env-like ORF of Cyclops2, suggesting that it serves a similar purpose. No other potential targeting peptide stands out from the sequence that has been analyzed so far. There is a conserved region that is predicted to be a transmembrane domain near the center of the Calypso env-like protein and a second transmembrane domain located at variable positions near the C-terminus. These may be the fusion and anchor functions of a TM peptide. It should also be noted that five of the seven ORFs are predicted to have a transmembrane domain that is just before and includes the first methionine. This N-terminal transmembrane domain may be a secretory signal of an SU peptide. The program TMpred estimates these transmembrane domains to be significant based on a score >500 (Hofmann and Stoffel (1993) Biol. Chem. 374:166). These three transmembrane domains are found in the Cyclops2 env-like protein at similar locations but at a reduced significance score. Another feature of the Calypso env-like ORF is the conserved splice site that is predicted to be at the first methionine by the program NetGene2 v. 2.4 with a confidence level of 1.00 (Hebsgaard et al. (1996) Nucleic Acids Res. 24: 3439-3452); Brunak et al. (1991) J. Mol. Biol 220: 49-65). There are other less preferred putative splice sites in the region, but only the splice site near the methionine is optimally placed and conserved in all seven env-like ORFs.

Example 4 Obtaining the Generic Plant Retroelements (“Generic” Elements)

[0270] ClustalX v1.63b (Thompson et al. (1994) Nucl. Acids Res. 22: 4673-4680) was used to align nucleotide sequences of Calypso1-1, Calypso1-2 and Calypso1-3. A consensus sequence was generated from the ClustalX output. The consensus sequence file was then translated and compared using ClustalX to amino acid sequences of retrovirus-like elements from soybean, pea (Cyclops2) and A. thaliana (Athila-like elements) using the GCG computer software package (Devereux et al. (1984) Nucleic Acids Res. 12: 387-395). For coding regions encompassing protease, reverse transcriptase and integrase, a new consensus sequence was generated that best matched the coding information in all elements. This second consensus sequence forms the protease, reverse transcriptase and integrase genes of the generic element. The gag gene of the generic element is a consensus sequence generated by editing alignments between Calypso1-1 and Calypso2-2. The env gene is a consensus sequence based on env gene sequence alignments of all Calypso elements. All non-coding regions for the generic element were obtained >from Calypso1-2, with the exception of the LTRs, which were taken from Calypso1-1.

[0271] A generic retrovirus will be constructed by first generating a DNA sequence that approximates the sequence of the generic element. An element that closely matches the consensus—for example, Calypso1-1—will be modified by PCR-based site-directed mutagenesis (Ausubel et al., Current Protocols in Molecular Biology (Greene Publishing Associates, Inc., 1993). Modifications will be sequentially introduced into the starting element until it conforms to the sequence of the generic element.

[0272] The generic element will be modified so that it will be expressed at high levels in plant cells. This will be accomplished by inserting an enhancer—such as the cauliflower mosaic virus 35S enhancer—into the 5′ LTR. To monitor replication, a marker gene will be inserted into the virus between the end of the coding region for the env gene and the polypurine tract. The marker gene may encode resistance to an herbicide or antibiotic. The modified generic element will then be introduced into plant cells by standard means of plant transformation. Because the modified generic element will be expressed at high levels, retroviral particles will be produced by the host plant cell. These will be harvested and purified by passing cell lysates over sucrose density gradients.

[0273] The plant retroviral particles will be incubated in the presence of non-transformed plant cells. The virus will associate with the plant cell and fuse with the plant cell membrane. The mRNA carried by the virus will be reverse transcribed and the resultant cDNA will be integrated into the genome of the plant. The integration of the viral DNA and the expression of the marker gene it carries will confer antibiotic resistance to the plant cell. Cells that carry integrated viruses can be identified through genetic selection.

[0274] Although the present invention has been fully described herein, it is to be noted that various changes and modifications are apparent to those skilled in the art. Such changes and modifications are to be understood as included within the scope of the present invention as defined by the appended claims.

1 41 1 18 DNA Glycine max 1 tggcgccgtt gccaattg 18 2 18 DNA Glycine max 2 tggcgccgtt gtcgggga 18 3 6 DNA Glycine max 3 ttgggg 6 4 7 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 4 Met Ala Ser Arg Lys Arg Lys 1 5 5 1263 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 5 atggcctccc gtaaacgcaa agctgtgccc acacccgggg aagcgtccaa ctgggactct 60 tcacgtttca ctttcgagat tgcttggcac agataccagg atagcattca gctccggaac 120 atccttccag agaggaatgt agagcttgga ccagggatgt ttgatgagtt cctgcaggaa 180 ctccagaggc tcagatggga ccaggttctg acccgacttc cagagaagtg gattgatgtt 240 gctctggtga aggagtttta ctccaaccta tatgatccag aggaccacag tccgaagttt 300 tggagtgttc gaggacaggt tgtgagattt gatgctgaga cgattaatga tttcctcgac 360 accccggtca tcttggcaga gggagaggat tatccagcct actctcagta cctcagcact 420 cctccagacc atgatgccat cctttccgct ctgtgtactc cagggggacg atttgttctg 480 aatgttgata gtgccccctg gaagctgctg cggaaggatc tgatgacgct cgcgcagaca 540 tggagtgtgc tctcttattt taaccttgca ctgacttttc acacttctga tattaatgtt 600 gacagggccc gactcaatta tggcttggtg atgaagatgg acctggacgt gggcagcctc 660 atttctcttc agatcagtca gatcgcccag tccatcactt ccaggcttgg gttcccagcg 720 ttgatcacaa cactgtgtga gattcagggg gttgtctctg ataccctgat ttttgagtca 780 ctcagtcctg tgatcaacct tgcctacatt aagaagaact gctggaaccc tgccgatcca 840 tctatcacat ttcaggggac ccgccgcacg cgcaccagag cttcggcgtc ggcatctgag 900 gctcctcttc catcccagca tccttctcag cctttttccc agagaccacg gcctccactt 960 ctatccacct cagcacctcc atacatgcat ggacagatgc tcaggtcctt gtaccagggt 1020 cagcagatca tcattcagaa cctgtatcga ttgtccctac atttgcagat ggatctgcca 1080 ctcatgactc cggaggccta tcgtcagcag gtcgccaagc taggagacca gccctccact 1140 gacagggggg aagagccttc tggagccgct gctactgagg atcctgccgt tgatgaagac 1200 ctcatagctg acttggctgg cgctgattgg agcccatggg cagacttggg cagaggcagc 1260 tga 1263 6 421 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 6 Met Ala Ser Arg Lys Arg Lys Ala Val Pro Thr Pro Gly Glu Ala Ser 1 5 10 15 Asn Trp Asp Ser Ser Arg Phe Thr Phe Glu Ile Ala Trp His Arg Tyr 20 25 30 Gln Asp Ser Ile Gln Leu Arg Asn Ile Leu Pro Glu Arg Asn Val Glu 35 40 45 Leu Gly Pro Gly Met Phe Asp Glu Phe Leu Gln Glu Leu Gln Arg Leu 50 55 60 Arg Trp Asp Gln Val Leu Thr Arg Leu Pro Glu Lys Trp Ile Asp Val 65 70 75 80 Ala Leu Val Lys Glu Phe Tyr Ser Asn Leu Tyr Asp Pro Glu Asp His 85 90 95 Ser Pro Lys Phe Trp Ser Val Arg Gly Gln Val Val Arg Phe Asp Ala 100 105 110 Glu Thr Ile Asn Asp Phe Leu Asp Thr Pro Val Ile Leu Ala Glu Gly 115 120 125 Glu Asp Tyr Pro Ala Tyr Ser Gln Tyr Leu Ser Thr Pro Pro Asp His 130 135 140 Asp Ala Ile Leu Ser Ala Leu Cys Thr Pro Gly Gly Arg Phe Val Leu 145 150 155 160 Asn Val Asp Ser Ala Pro Trp Lys Leu Leu Arg Lys Asp Leu Met Thr 165 170 175 Leu Ala Gln Thr Trp Ser Val Leu Ser Tyr Phe Asn Leu Ala Leu Thr 180 185 190 Phe His Thr Ser Asp Ile Asn Val Asp Arg Ala Arg Leu Asn Tyr Gly 195 200 205 Leu Val Met Lys Met Asp Leu Asp Val Gly Ser Leu Ile Ser Leu Gln 210 215 220 Ile Ser Gln Ile Ala Gln Ser Ile Thr Ser Arg Leu Gly Phe Pro Ala 225 230 235 240 Leu Ile Thr Thr Leu Cys Glu Ile Gln Gly Val Val Ser Asp Thr Leu 245 250 255 Ile Phe Glu Ser Leu Ser Pro Val Ile Asn Leu Ala Tyr Ile Lys Lys 260 265 270 Asn Cys Trp Asn Pro Ala Asp Pro Ser Ile Thr Phe Gln Gly Thr Arg 275 280 285 Arg Thr Arg Thr Arg Ala Ser Ala Ser Ala Ser Glu Ala Pro Leu Pro 290 295 300 Ser Gln His Pro Ser Gln Pro Phe Ser Gln Arg Pro Arg Pro Pro Leu 305 310 315 320 Leu Ser Thr Ser Ala Pro Pro Tyr Met His Gly Gln Met Leu Arg Ser 325 330 335 Leu Tyr Gln Gly Gln Gln Ile Ile Ile Gln Asn Leu Tyr Arg Leu Ser 340 345 350 Leu His Leu Gln Met Asp Leu Pro Leu Met Thr Pro Glu Ala Tyr Arg 355 360 365 Gln Gln Val Ala Lys Leu Gly Asp Gln Pro Ser Thr Asp Arg Gly Glu 370 375 380 Glu Pro Ser Gly Ala Ala Ala Thr Glu Asp Pro Ala Val Asp Glu Asp 385 390 395 400 Leu Ile Ala Asp Leu Ala Gly Ala Asp Trp Ser Pro Trp Ala Asp Leu 405 410 415 Gly Arg Gly Ser Glx 420 7 1596 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 7 atgcgaggta gaactgcatc tggagacgtt gttcctatta acttagaaat tgaagctacg 60 tgtcggcgta acaacgctgc aagaagaaga agggagcaag acatagaagg aagtagttac 120 acctcacctc ctccttctcc aaattatgct cagatggacg gggaaccggc acaaagagtc 180 acactagagg acttctctaa taccaccact cctcagttct ttacaagtat cacaaggccg 240 gaagtccaag cagatctcct tactcaaggg aacctcttcc atggtcttcc aaatgaagat 300 ccatatgcgc atctagcctc atacatagag atatgcagca ccgttaaaat cgccggagtt 360 ccaaaagatg cgatactcct taacctcttt tccttttccc tagcaggaga ggcaaaaaga 420 tggttgcact cctttaaagg caatagctta agaacatggg aagaagtagt ggaaaaattc 480 ttaaagaagt atttcccaga gtcaaagacc gtcgaacgaa agatggagat ttcttatttc 540 catcaatttc tggatgaatc ccttagcgaa gcactagacc atttccacgg attgctaaga 600 aaaacaccaa cacacagata cagcgagcca gtacaactaa acatattcat cgatgacttg 660 caactcttaa tcgaaacagc tactagaggg aagatcaagc tgaagactcc cgaagaagcg 720 atggagctcg tcgagaacat ggcggctagc gatcaagcaa tccttcatga tcacacttat 780 gttcccacaa aaagaagcct cttggagctt agcacgcagg acgcaacttt ggtacaaaac 840 aagctgttga cgaggcagat agaagccctc atcgaaaccc tcagcaagct gcctcaacaa 900 ttacaagcga taagttcttc ccactcttct gttttgcagg tagaagaatg ccccacatgc 960 agagggacac atgagcctgg acaatgtgca agccaacaag acccctctcg tgaagtaaat 1020 tatataggca tactaaatcg ttacggattt cagggctaca accagggaaa tccatctgga 1080 ttcaatcaag gggcaacaag atttaatcac gagccaccgg ggtttaatca aggaagaaac 1140 ttcatgcaag gctcaagttg gacgaataaa ggaaatcaat ataaggagca aaggaaccaa 1200 ccaccatacc agccaccata ccagcaccct agccaaggtc cgaatcagca agaaaagccc 1260 accaaaatag aggaactgct gctgcaattc atcaaggaga caagatcaca tcaaaagagc 1320 acggatgcag ccattcggaa tctagaagtt caaatgggcc aactggcgca tgacaaagcc 1380 gaacggccca ctagaacttt cggtgctaac atggagagaa gaaccccaag gaaggataaa 1440 gcagtactga ctagagggca gagaagagcg caggaggagg gtaaggttga aggagaagac 1500 tggccagaag aaggaaggac agagaagaca gaagaagaag agaaggtggc agaagaacct 1560 aagcgtacca agagccagag agcaagggaa gccaag 1596 8 532 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 8 Met Arg Gly Arg Thr Ala Ser Gly Asp Val Val Pro Ile Asn Leu Glu 1 5 10 15 Ile Glu Ala Thr Cys Arg Arg Asn Asn Ala Ala Arg Arg Arg Arg Glu 20 25 30 Gln Asp Ile Glu Gly Ser Ser Tyr Thr Ser Pro Pro Pro Ser Pro Asn 35 40 45 Tyr Ala Gln Met Asp Gly Glu Pro Ala Gln Arg Val Thr Leu Glu Asp 50 55 60 Phe Ser Asn Thr Thr Thr Pro Gln Phe Phe Thr Ser Ile Thr Arg Pro 65 70 75 80 Glu Val Gln Ala Asp Leu Leu Thr Gln Gly Asn Leu Phe His Gly Leu 85 90 95 Pro Asn Glu Asp Pro Tyr Ala His Leu Ala Ser Tyr Ile Glu Ile Cys 100 105 110 Ser Thr Val Lys Ile Ala Gly Val Pro Lys Asp Ala Ile Leu Leu Asn 115 120 125 Leu Phe Ser Phe Ser Leu Ala Gly Glu Ala Lys Arg Trp Leu His Ser 130 135 140 Phe Lys Gly Asn Ser Leu Arg Thr Trp Glu Glu Val Val Glu Lys Phe 145 150 155 160 Leu Lys Lys Tyr Phe Pro Glu Ser Lys Thr Val Glu Arg Lys Met Glu 165 170 175 Ile Ser Tyr Phe His Gln Phe Leu Asp Glu Ser Leu Ser Glu Ala Leu 180 185 190 Asp His Phe His Gly Leu Leu Arg Lys Thr Pro Thr His Arg Tyr Ser 195 200 205 Glu Pro Val Gln Leu Asn Ile Phe Ile Asp Asp Leu Gln Leu Leu Ile 210 215 220 Glu Thr Ala Thr Arg Gly Lys Ile Lys Leu Lys Thr Pro Glu Glu Ala 225 230 235 240 Met Glu Leu Val Glu Asn Met Ala Ala Ser Asp Gln Ala Ile Leu His 245 250 255 Asp His Thr Tyr Val Pro Thr Lys Arg Ser Leu Leu Glu Leu Ser Thr 260 265 270 Gln Asp Ala Thr Leu Val Gln Asn Lys Leu Leu Thr Arg Gln Ile Glu 275 280 285 Ala Leu Ile Glu Thr Leu Ser Lys Leu Pro Gln Gln Leu Gln Ala Ile 290 295 300 Ser Ser Ser His Ser Ser Val Leu Gln Val Glu Glu Cys Pro Thr Cys 305 310 315 320 Arg Gly Thr His Glu Pro Gly Gln Cys Ala Ser Gln Gln Asp Pro Ser 325 330 335 Arg Glu Val Asn Tyr Ile Gly Ile Leu Asn Arg Tyr Gly Phe Gln Gly 340 345 350 Tyr Asn Gln Gly Asn Pro Ser Gly Phe Asn Gln Gly Ala Thr Arg Phe 355 360 365 Asn His Glu Pro Pro Gly Phe Asn Gln Gly Arg Asn Phe Met Gln Gly 370 375 380 Ser Ser Trp Thr Asn Lys Gly Asn Gln Tyr Lys Glu Gln Arg Asn Gln 385 390 395 400 Pro Pro Tyr Gln Pro Pro Tyr Gln His Pro Ser Gln Gly Pro Asn Gln 405 410 415 Gln Glu Lys Pro Thr Lys Ile Glu Glu Leu Leu Leu Gln Phe Ile Lys 420 425 430 Glu Thr Arg Ser His Gln Lys Ser Thr Asp Ala Ala Ile Arg Asn Leu 435 440 445 Glu Val Gln Met Gly Gln Leu Ala His Asp Lys Ala Glu Arg Pro Thr 450 455 460 Arg Thr Phe Gly Ala Asn Met Glu Arg Arg Thr Pro Arg Lys Asp Lys 465 470 475 480 Ala Val Leu Thr Arg Gly Gln Arg Arg Ala Gln Glu Glu Gly Lys Val 485 490 495 Glu Gly Glu Asp Trp Pro Glu Glu Gly Arg Thr Glu Lys Thr Glu Glu 500 505 510 Glu Glu Lys Val Ala Glu Glu Pro Lys Arg Thr Lys Ser Gln Arg Ala 515 520 525 Arg Glu Ala Lys 530 9 603 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 9 tgtgataaat gccagagaac aggggggata tctcgaagaa atgagatgcc tttgcagaat 60 atcatggaag tagagatctt tgactgttgg ggcatagact tcatggggcc ttttccttcg 120 tcatacggga atgtctacat cttggtagct gtggattacg tctccaaatg ggtggaagcc 180 atagccacgc caaaggacga tgccagggta gtgatcaaat ttctgaagaa gaacattttt 240 tcccgttttg gagtcccacg agccttgatt agtgataggg gaacgcactt ctgcaacaat 300 cagttgaaga aagtcctgga gcactataat gtccgacata aggtggccac accttatcac 360 cctcagacaa atggccaagc agaaatttct aacagggagc tcaagcgaat cctggaaaag 420 acagttgcat caacaagaaa ggattggtcc ttgaagctcg atgatgctct ctgggcctat 480 aggacagcgt tcaagactcc catcggctta tcaccatttc agctagtgta tgggaaggca 540 tgtcatttac cagtggagct ggagtacaaa gcatattggg ctctcaagtt gctcaacttt 600 gac 603 10 201 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 10 Cys Asp Lys Cys Gln Arg Thr Gly Gly Ile Ser Arg Arg Asn Glu Met 1 5 10 15 Pro Leu Gln Asn Ile Met Glu Val Glu Ile Phe Asp Cys Trp Gly Ile 20 25 30 Asp Phe Met Gly Pro Phe Pro Ser Ser Tyr Gly Asn Val Tyr Ile Leu 35 40 45 Val Ala Val Asp Tyr Val Ser Lys Trp Val Glu Ala Ile Ala Thr Pro 50 55 60 Lys Asp Asp Ala Arg Val Val Ile Lys Phe Leu Lys Lys Asn Ile Phe 65 70 75 80 Ser Arg Phe Gly Val Pro Arg Ala Leu Ile Ser Asp Arg Gly Thr His 85 90 95 Phe Cys Asn Asn Gln Leu Lys Lys Val Leu Glu His Tyr Asn Val Arg 100 105 110 His Lys Val Ala Thr Pro Tyr His Pro Gln Thr Asn Gly Gln Ala Glu 115 120 125 Ile Ser Asn Arg Glu Leu Lys Arg Ile Leu Glu Lys Thr Val Ala Ser 130 135 140 Thr Arg Lys Asp Trp Ser Leu Lys Leu Asp Asp Ala Leu Trp Ala Tyr 145 150 155 160 Arg Thr Ala Phe Lys Thr Pro Ile Gly Leu Ser Pro Phe Gln Leu Val 165 170 175 Tyr Gly Lys Ala Cys His Leu Pro Val Glu Leu Glu Tyr Lys Ala Tyr 180 185 190 Trp Ala Leu Lys Leu Leu Asn Phe Asp 195 200 11 600 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 11 ttggaggctg ggctcatata ccccatctct gacagcgctt gggtaagccc agtacaggtg 60 gttcccaaga aaggtggaat gacagtggta cgagatgaga ggaatgactt gataccaaca 120 cgaactgtca ctggttggcg aatgtgtatc gactatcgca agctgaatga agccacacgg 180 aaggaccatt tccccttacc tttcatggat cagatgctgg agagacttgc agggcaggca 240 tactactgtt tcttggatgg atactcggga tacaaccaga tcgcggtaga ccccagagat 300 caggagaaga cggcctttac atgccccttt ggcgtctttg cttacagaag gatgccattc 360 gggttatgta atgcaccagc cacatttcag aggtgcatgc tggccatttt ttcagacatg 420 gtggagaaaa gcatcgaggt atttatggac gacttctcgg tttttggacc ctcatttgac 480 agctgtttga ggaacctaga gagggtactt cagaggtgcg aagagactaa cttggtactg 540 aattgggaaa agtgtcattt catggttcga gagggcatag tcctaggcca caagatctca 600 12 200 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 12 Leu Glu Ala Gly Leu Ile Tyr Pro Ile Ser Asp Ser Ala Trp Val Ser 1 5 10 15 Pro Val Gln Val Val Pro Lys Lys Gly Gly Met Thr Val Val Arg Asp 20 25 30 Glu Arg Asn Asp Leu Ile Pro Thr Arg Thr Val Thr Gly Trp Arg Met 35 40 45 Cys Ile Asp Tyr Arg Lys Leu Asn Glu Ala Thr Arg Lys Asp His Phe 50 55 60 Pro Leu Pro Phe Met Asp Gln Met Leu Glu Arg Leu Ala Gly Gln Ala 65 70 75 80 Tyr Tyr Cys Phe Leu Asp Gly Tyr Ser Gly Tyr Asn Gln Ile Ala Val 85 90 95 Asp Pro Arg Asp Gln Glu Lys Thr Ala Phe Thr Cys Pro Phe Gly Val 100 105 110 Phe Ala Tyr Arg Arg Met Pro Phe Gly Leu Cys Asn Ala Pro Ala Thr 115 120 125 Phe Gln Arg Cys Met Leu Ala Ile Phe Ser Asp Met Val Glu Lys Ser 130 135 140 Ile Glu Val Phe Met Asp Asp Phe Ser Val Phe Gly Pro Ser Phe Asp 145 150 155 160 Ser Cys Leu Arg Asn Leu Glu Arg Val Leu Gln Arg Cys Glu Glu Thr 165 170 175 Asn Leu Val Leu Asn Trp Glu Lys Cys His Phe Met Val Arg Glu Gly 180 185 190 Ile Val Leu Gly His Lys Ile Ser 195 200 13 858 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 13 aaggaagaac cactagccct tccacaggat ctcccatatc ctatggcacc caccaagaag 60 aacaaggagc gttactttgc acgtttcttg gaaatattca aagggttaga aatcactatg 120 ccattcgggg aagccttaca gcagatgccc ctctactcca aatttatgaa agacatcctc 180 accaagaagg ggaagtatat tgacaacgag aatattgtgg taggaggcaa ttgcagtgcg 240 ataatacaaa ggattctacc caagaagttt aaagaccccg gaagtgttac catcccgtgc 300 accattggga aggaagccgt aaacaaggcc ctcattgatc taggagcaag tatcaatctg 360 atgcccttgt caatgtgcaa aagaattggg aatttgaaga tagatcccac caagatgacg 420 cttcaactgg cagaccgctc aatcacaagg ccatatgggg tggtagaaga tgtcctggtc 480 aaggtacgcc acttcacttt tccggtggac tttgttatca tggatatcga agaagacact 540 gagattcccc ttatcttagg cagacccttc atgctgactg ccaactgtgt ggtggatatg 600 gggaaaggga acttagagtt gactattgat aatcagaaga tcacctttga ccttatcaag 660 gcaatgaagt acccacagga gggttggaag tgcttcagaa tagaggagat tgatgaggaa 720 gatgtcagtt ttctcgagac accaaagact tcgctagaaa aagcaatggt aaatcattta 780 gactgtctaa ccagtgaaga ggaagaagat ctgaaggctt gcttggaaaa cttggatcaa 840 gaagacagta ttcctgag 858 14 286 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 14 Lys Glu Glu Pro Leu Ala Leu Pro Gln Asp Leu Pro Tyr Pro Met Ala 1 5 10 15 Pro Thr Lys Lys Asn Lys Glu Arg Tyr Phe Ala Arg Phe Leu Glu Ile 20 25 30 Phe Lys Gly Leu Glu Ile Thr Met Pro Phe Gly Glu Ala Leu Gln Gln 35 40 45 Met Pro Leu Tyr Ser Lys Phe Met Lys Asp Ile Leu Thr Lys Lys Gly 50 55 60 Lys Tyr Ile Asp Asn Glu Asn Ile Val Val Gly Gly Asn Cys Ser Ala 65 70 75 80 Ile Ile Gln Arg Ile Leu Pro Lys Lys Phe Lys Asp Pro Gly Ser Val 85 90 95 Thr Ile Pro Cys Thr Ile Gly Lys Glu Ala Val Asn Lys Ala Leu Ile 100 105 110 Asp Leu Gly Ala Ser Ile Asn Leu Met Pro Leu Ser Met Cys Lys Arg 115 120 125 Ile Gly Asn Leu Lys Ile Asp Pro Thr Lys Met Thr Leu Gln Leu Ala 130 135 140 Asp Arg Ser Ile Thr Arg Pro Tyr Gly Val Val Glu Asp Val Leu Val 145 150 155 160 Lys Val Arg His Phe Thr Phe Pro Val Asp Phe Val Ile Met Asp Ile 165 170 175 Glu Glu Asp Thr Glu Ile Pro Leu Ile Leu Gly Arg Pro Phe Met Leu 180 185 190 Thr Ala Asn Cys Val Val Asp Met Gly Lys Gly Asn Leu Glu Leu Thr 195 200 205 Ile Asp Asn Gln Lys Ile Thr Phe Asp Leu Ile Lys Ala Met Lys Tyr 210 215 220 Pro Gln Glu Gly Trp Lys Cys Phe Arg Ile Glu Glu Ile Asp Glu Glu 225 230 235 240 Asp Val Ser Phe Leu Glu Thr Pro Lys Thr Ser Leu Glu Lys Ala Met 245 250 255 Val Asn His Leu Asp Cys Leu Thr Ser Glu Glu Glu Glu Asp Leu Lys 260 265 270 Ala Cys Leu Glu Asn Leu Asp Gln Glu Asp Ser Ile Pro Glu 275 280 285 15 192 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 15 tttgaactaa tgtgtgatgc cagtgattat gcagtaggag cagttttggg acagaggaaa 60 gacaaggtat ttcacgccat ctattatgct agcaaggtcc tgaatgaagc acagttgaat 120 tatgcaacca cagaaaagga gatgctagcc attgtctttg ccttggagaa gttcaggtca 180 tacttgatag gg 192 16 64 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 16 Phe Glu Leu Met Cys Asp Ala Ser Asp Tyr Ala Val Gly Ala Val Leu 1 5 10 15 Gly Gln Arg Lys Asp Lys Val Phe His Ala Ile Tyr Tyr Ala Ser Lys 20 25 30 Val Leu Asn Glu Ala Gln Leu Asn Tyr Ala Thr Thr Glu Lys Glu Met 35 40 45 Leu Ala Ile Val Phe Ala Leu Glu Lys Phe Arg Ser Tyr Leu Ile Gly 50 55 60 17 12286 DNA Artificial Sequence Description of Artificial Sequence plant retroelement sequence 17 tgataactgc taaataattg tgaattaata gtagaaaatt agtcaaattt tggcttaaaa 60 ttaattattt agcagttatt tgtgattaaa agttagaaaa gcaattaagt tgaatttttg 120 gccatagata tgaaaactga aggtacaaca agcaaaaggc agcagaaagt gaagaaaaag 180 aataaaatct gaagcagacc cagcccaaca cgcgccctta gcgcgcgtca cgcgctaagc 240 ttgcaaggca gcacaggcac taagcgaggc gttaagcacg aagatgcagg attcgttacg 300 tgcgctaagc gcgaggcaca cgctaagcgc gcgatccaac agaagcacac gctaagcctg 360 cagcatgcgc taagcgcgcc tacgaaggcc caaagcccat ttctacacct ataaatagag 420 atccaagcca agggagaatg tacaccttgc ctcagagcac ttctctcagc attccaagct 480 tgagctctcc cttttctctc tatattcttt gcttttatta tccattcttt ctttcacccc 540 agttgtaaag cccctcaatg gccatgagtg gttaatcccc tagctacggc ctggtaggcc 600 taaaaagcca atgatgtatg gtgtacttca agagttatca atgcaaagag gattcattcc 660 aggttttatg ttctaattct ttccttttta tcttgcattt atgtcttaaa tttctgttgg 720 gttttattcg ctcgggagag ggtatttcct aataagggtt taagaagtaa tgcatgcatc 780 agttttaggg gttatacgct tggtaaaggg taacacctaa tagaacaaat taagaaaagg 840 atcgtcgggc tagcattgct aggcatagaa tgatggccca atgcccatgc atttagcaac 900 atctagaatt taaccttaat gcattttaat tattgaatct tcacaaaggc atttgggaga 960 taggtagtta aaataggctt gtcatcgtga ggcatcaagg gcaagtaaaa ttaatagatg 1020 tgggtagaac taattcaact gcattggtaa tgaacatcat aaattcattc atcgtaggcc 1080 aattaggttt gtccggtctt ggcattttca tcaattgtct tcctaaatta tttgatctaa 1140 tagcaacaat ttattcttat gcctattcct gtttttacta tttactttta cttacaaatt 1200 gaagagtatt caataaagtg caataaaatc cctatggaaa cgatactcgg acttccgaga 1260 attactactt agaacgattt ggtacacttg tcaaacacct caacaagttt ttggcgccgt 1320 tgtcggggat tttgttctcg cacttaattg ccatactata ttagtttgta agcttaattc 1380 ttcttttctt ggctcattct tttattattc tttactttac tttttcttct atcctttctt 1440 tcttctccca taaattgcac gggtagtgcc tttttgtttt tatgcgaggt agaactgcat 1500 ctggagacgt tgttcctatt aacttagaaa ttgaagctac gtgtcggcgt aacaacgctg 1560 caagaagaag aagggagcaa gacatagaag gaagtagtta cacctcacct cctccttctc 1620 caaattatgc tcagatggac ggggaaccgg cacaaagagt cacactagag gacttctcta 1680 ataccaccac tcctcagttc tttacaagta tcacaaggcc ggaagtccaa gcagatctcc 1740 ttactcaagg gaacctcttc catggtcttc caaatgaaga tccatatgcg catctagcct 1800 catacataga gatatgcagc accgttaaaa tcgccggagt tccaaaagat gcgatactcc 1860 ttaacctctt ttccttttcc ctagcaggag aggcaaaaag atggttgcac tcctttaaag 1920 gcaatagctt aagaacatgg gaagaagtag tggaaaaatt cttaaagaag tatttcccag 1980 agtcaaagac cgtcgaacga aagatggaga tttcttattt ccatcaattt ctggatgaat 2040 cccttagcga agcactagac catttccacg gattgctaag aaaaacacca acacacagat 2100 acagcgagcc agtacaacta aacatattca tcgatgactt gcaactctta atcgaaacag 2160 ctactagagg gaagatcaag ctgaagactc ccgaagaagc gatggagctc gtcgagaaca 2220 tggcggctag cgatcaagca atccttcatg atcacactta tgttcccaca aaaagaagcc 2280 tcttggagct tagcacgcag gacgcaactt tggtacaaaa caagctgttg acgaggcaga 2340 tagaagccct catcgaaacc ctcagcaagc tgcctcaaca attacaagcg ataagttctt 2400 cccactcttc tgttttgcag gtagaagaat gccccacatg cagagggaca catgagcctg 2460 gacaatgtgc aagccaacaa gacccctctc gtgaagtaaa ttatataggc atactaaatc 2520 gttacggatt tcagggctac aaccagggaa atccatctgg attcaatcaa ggggcaacaa 2580 gatttaatca cgagccaccg gggtttaatc aaggaagaaa cttcatgcaa ggctcaagtt 2640 ggacgaataa aggaaatcaa tataaggagc aaaggaacca accaccatac cagccaccat 2700 accagcaccc tagccaaggt ccgaatcagc aagaaaagcc caccaaaata gaggaactgc 2760 tgctgcaatt catcaaggag acaagatcac atcaaaagag cacggatgca gccattcgga 2820 atctagaagt tcaaatgggc caactggcgc atgacaaagc cgaacggccc actagaactt 2880 tcggtgctaa catggagaga agaaccccaa ggaaggataa agcagtactg actagagggc 2940 agagaagagc gcaggaggag ggtaaggttg aaggagaaga ctggccagaa gaaggaagga 3000 cagagaagac agaagaagaa gagaaggtgg cagaagaacc taagcgtacc aagagccaga 3060 gagcaaggga agccaagaag gaagaaccac tagcccttcc acaggatctc ccatatccta 3120 tggcacccac caagaagaac aaggagcgtt actttgcacg tttcttggaa atattcaaag 3180 ggttagaaat cactatgcca ttcggggaag ccttacagca gatgcccctc tactccaaat 3240 ttatgaaaga catcctcacc aagaagggga agtatattga caacgagaat attgtggtag 3300 gaggcaattg cagtgcgata atacaaagga ttctacccaa gaagtttaaa gaccccggaa 3360 gtgttaccat cccgtgcacc attgggaagg aagccgtaaa caaggccctc attgatctag 3420 gagcaagtat caatctgatg cccttgtcaa tgtgcaaaag aattgggaat ttgaagatag 3480 atcccaccaa gatgacgctt caactggcag accgctcaat cacaaggcca tatggggtgg 3540 tagaagatgt cctggtcaag gtacgccact tcacttttcc ggtggacttt gttatcatgg 3600 atatcgaaga agacactgag attcccctta tcttaggcag acccttcatg ctgactgcca 3660 actgtgtggt ggatatgggg aaagggaact tagagttgac tattgataat cagaagatca 3720 cctttgacct tatcaaggca atgaagtacc cacaggaggg ttggaagtgc ttcagaatag 3780 aggagattga tgaggaagat gtcagttttc tcgagacacc aaagacttcg ctagaaaaag 3840 caatggtaaa tcatttagac tgtctaacca gtgaagagga agaagatctg aaggcttgct 3900 tggaaaactt ggatcaagaa gacagtattc ctgagggaga agccaatttc gaggagctag 3960 agaaggaagt tccgtctgag aagccgaaga tagagttgaa gatattgcct gatcatctga 4020 agtatgtgtt cttggaggaa gataaaccta tagtgatcag taacgcactc acaacagagg 4080 aggaaaatag gttggtagat gtcctcaaga aacacaggga agcaattgga tggcacatat 4140 cggatctcaa ggaaattagc cctgcttact gcatgcacag gataatgatg gaagaggact 4200 acaagccagt ccgacaaccc cagaggcggc tgaatccaac aatgaaggaa gaggtaagaa 4260 aggaggtact caagctcttg gaggctgggc tcatataccc catctctgac agcgcttggg 4320 taagcccagt acaggtggtt cccaagaaag gtggaatgac agtggtacga gatgagagga 4380 atgacttgat accaacacga actgtcactg gttggcgaat gtgtatcgac tatcgcaagc 4440 tgaatgaagc cacacggaag gaccatttcc ccttaccttt catggatcag atgctggaga 4500 gacttgcagg gcaggcatac tactgtttct tggatggata ctcgggatac aaccagatcg 4560 cggtagaccc cagagatcag gagaagacgg cctttacatg cccctttggc gtctttgctt 4620 acagaaggat gccattcggg ttatgtaatg caccagccac atttcagagg tgcatgctgg 4680 ccattttttc agacatggtg gagaaaagca tcgaggtatt tatggacgac ttctcggttt 4740 ttggaccctc atttgacagc tgtttgagga acctagagag ggtacttcag aggtgcgaag 4800 agactaactt ggtactgaat tgggaaaagt gtcatttcat ggttcgagag ggcatagtcc 4860 taggccacaa gatctcagcc agagggattg aggttgatcg ggcaaagata gacgtcatcg 4920 agaagctgcc accaccactg aatgttaaag gggttagaag tttcttaggg catgcaggtt 4980 tctacaggag gtttatcaag gacttctcga agattgccag gcccttaagc aatctgttga 5040 ataaagacgt ggcttttgtg tttgatgaag aatgtttagc agcatttcaa tcactgaaga 5100 ataagctcgt cactgcaccc gtaatgattg cacccgactg gaataaagat tttgaactaa 5160 tgtgtgatgc cagtgattat gcagtaggag cagttttggg acagaggaaa gacaaggtat 5220 ttcacgccat ctattatgct agcaaggtcc tgaatgaagc acagttgaat tatgcaacca 5280 cagaaaagga gatgctagcc attgtctttg ccttggagaa gttcaggtca tacttgatag 5340 ggtcgagggt catcatttac acagatcatg ctgccatcaa gcacctgctc gccaaaacag 5400 actcaaagcc gaggttgatt agatgggtcc tgctgttaca agaatttgac atcatcatca 5460 aggacaagaa aggatccgag aatgtggtag ccaatcatct atctcgatta aagaatgaag 5520 aagtcaccaa ggaagaacca gaggtaaaag gtgaatttcc tgatgagttt cttttgcagg 5580 ttaccgaaag accttggttt gcagacatgg ctaactacaa agccacggga gtcattccag 5640 aggagtttaa ttggagtcag aggaagaaat tcttgcacga tgcacgcttc tatgtgtggg 5700 atgatcctca tttgttcaag gcaggagcag ataatttatt aaggagatgc gtcacaaagg 5760 aggaagcacg gagcattctt tggcactgcc acagttcacc ctatggcgga caccacagtg 5820 gggacagaac agcagcaaaa gtgctacaat caggtttttt ctggccctct atttttaaag 5880 atgctcacga gtttgtgcgt tgttgtgata aatgccagag aacagggggg atatctcgaa 5940 gaaatgagat gcctttgcag aatatcatgg aagtagagat ctttgactgt tggggcatag 6000 acttcatggg gccttttcct tcgtcatacg ggaatgtcta catcttggta gctgtggatt 6060 acgtctccaa atgggtggaa gccatagcca cgccaaagga cgatgccagg gtagtgatca 6120 aatttctgaa gaagaacatt ttttcccgtt ttggagtccc acgagccttg attagtgata 6180 ggggaacgca cttctgcaac aatcagttga agaaagtcct ggagcactat aatgtccgac 6240 ataaggtggc cacaccttat caccctcaga caaatggcca agcagaaatt tctaacaggg 6300 agctcaagcg aatcctggaa aagacagttg catcaacaag aaaggattgg tccttgaagc 6360 tcgatgatgc tctctgggcc tataggacag cgttcaagac tcccatcggc ttatcaccat 6420 ttcagctagt gtatgggaag gcatgtcatt taccagtgga gctggagtac aaagcatatt 6480 gggctctcaa gttgctcaac tttgacaaca acgcatgcgg ggaaaagagg aagctacagc 6540 tgctggaatt agaagagatg agactgaatg cctacgagtc atccaaaatt tacaaggaaa 6600 agatgaaggc atatcatgac aagaagctac tgaggaaaga attccagcca gggcagcagg 6660 tattactctt taactcaagg ctaaggctat tcccaggtaa gctgaagtcc aagtggtcag 6720 ggccattcat aatcaaagaa gtcagacctt acggagcagt agaattggtg gaccctagag 6780 aagaggactt tgagaagaaa tggatcgtca atggacagcg cttgaagcct tataacggag 6840 gacaactaga gcgattgacg accatcatct acttaaatga cccttgagaa ggcctactgt 6900 ctagctaaag acaataaact aagcgctggt tgggaggcaa cccaacatat tttgtaaaaa 6960 tgtagttatc tttattctat gtaaaaaaaa aaaaaaagcc caataggtgc aaataggaaa 7020 caggaggtgc aaaaagcaaa ggcccaacag gtgaagacaa caataggagg ggtgccaata 7080 gcaaaactga agtgggctgc acgaagccac gcgcccaatt cttggtcttt tcacacaaaa 7140 caatcactaa cgaaggtaaa gaattgcttt gtatggatgt tgttatgaat gcacaggtaa 7200 cagcacgcta agccctgctc gacgcttagc caatgaagac ggattgaagg ccataacgac 7260 gagctcgtta agcgtgacga agcacgctaa gcaggcgcct gacaggacga gaaagcaaag 7320 cgcgcgctta gccggcactt ccgcgctaag cgcgctcatg aacatcactg aacgcgctaa 7380 acgtgtgcca gaggcgctaa acgcgtgcca gaggcgctaa acgcgtgcat tagtcacagc 7440 aggatggtgc taagcgcggg gttgggcctc agggcccatc aaccctcgca ccttacttgt 7500 tgcaccccta tttctactat tcccactccc ttctaatttc tttttgcacc ccccttcttt 7560 actgactgca cctctatttt gattactttt tgcacccccc ctgattgcta acttcagact 7620 atctttcttg ttttttgttt ttttggtttt ttggtcagat ggcctcccgt aaacgcaaag 7680 ctgtgcccac acccggggaa gcgtccaact gggactcttc acgtttcact ttcgagattg 7740 cttggcacag ataccaggat agcattcagc tccggaacat ccttccagag aggaatgtag 7800 agcttggacc agggatgttt gatgagttcc tgcaggaact ccagaggctc agatgggacc 7860 aggttctgac ccgacttcca gagaagtgga ttgatgttgc tctggtgaag gagttttact 7920 ccaacctata tgatccagag gaccacagtc cgaagttttg gagtgttcga ggacaggttg 7980 tgagatttga tgctgagacg attaatgatt tcctcgacac cccggtcatc ttggcagagg 8040 gagaggatta tccagcctac tctcagtacc tcagcactcc tccagaccat gatgccatcc 8100 tttccgctct gtgtactcca gggggacgat ttgttctgaa tgttgatagt gccccctgga 8160 agctgctgcg gaaggatctg atgacgctcg cgcagacatg gagtgtgctc tcttatttta 8220 accttgcact gacttttcac acttctgata ttaatgttga cagggcccga ctcaattatg 8280 gcttggtgat gaagatggac ctggacgtgg gcagcctcat ttctcttcag atcagtcaga 8340 tcgcccagtc catcacttcc aggcttgggt tcccagcgtt gatcacaaca ctgtgtgaga 8400 ttcagggggt tgtctctgat accctgattt ttgagtcact cagtcctgtg atcaaccttg 8460 cctacattaa gaagaactgc tggaaccctg ccgatccatc tatcacattt caggggaccc 8520 gccgcacgcg caccagagct tcggcgtcgg catctgaggc tcctcttcca tcccagcatc 8580 cttctcagcc tttttcccag agaccacggc ctccacttct atccacctca gcacctccat 8640 acatgcatgg acagatgctc aggtccttgt accagggtca gcagatcatc attcagaacc 8700 tgtatcgatt gtccctacat ttgcagatgg atctgccact catgactccg gaggcctatc 8760 gtcagcaggt cgccaagcta ggagaccagc cctccactga caggggggaa gagccttctg 8820 gagccgctgc tactgaggat cctgccgttg atgaagacct catagctgac ttggctggcg 8880 ctgattggag cccatgggca gacttgggca gaggcagctg atcttatgct ttaatgtttt 8940 cttttatatt atgtttgtgt tctcttttat gttttatgtt atgtttttat gtagtctgtt 9000 tggtaattaa aaagaggtag tagtaaaaat attagtattt cagtatgtgt tttctgagta 9060 ataagtgcat gataactcaa gcaatcataa ttctttagct tgttcagaaa ggttcaacac 9120 ttgagatgcc actgatcctt ggagaaacac tggttctgga agcaaaagtc aggtcaagaa 9180 atggaacatg aatagcacag agtggaaagg ttagcttgat ggaacaaggt cataactggt 9240 acgccgaata cttgtttaag tccctgtgag catggttgtc aaactctaga gtcaactcat 9300 agactctcat gagtttaaga gtttacttca gtcccgcgag ttgactcgga agcaaactcg 9360 cttttgagca aactcgtgga ctcggagtga actcatgtaa actcgtaaga gtctacgagt 9420 tgactctaga gtttgacaac catgcataag tgttcaaaat taaagcattt aaataattaa 9480 aaaaagcaca aatgtcttca aagaagcatg ttcaatcctc taataggatc atcttcatga 9540 atatcatcac tttcatcatc atctccatct ccatcatcat catcaaggtc ttcctcagat 9600 tgtgcatcat cattaggttc cacaaagatt aaattatcta gatcaaaagc ttaaaataga 9660 tatcaaatat gctatattag aaatagttaa aacttaaaat aatacacaag caaattttaa 9720 atatgagaaa gttcagaaat tatacctttt cttggtgtta ttaaagtttc attttatctt 9780 ctcttttgca ttttccatct cctcacatat gaaaagcata attctattga atttcagtaa 9840 caagtttgat ccaactccaa cattgtaagg tcagttgttg tgttttgtaa tagactaata 9900 tgaagtatga agtatgaact atgaacttat tgtcatctgt ttgcaaattg gtgcattttg 9960 aatatattta cttattatcc attttttttt ttttacgaag tagactctca cgagtctgcg 10020 tagactctcg atatcgataa ccttgccgat gagagtgtga acttaattgt gagagaaaat 10080 gcctattttt aagttcctgg ttttgcatca ttcttagacg gttagaatag ttacttaagg 10140 tggatatgat caaggccatg tttgtttgtt tacctactta gccaaaaagc caacctaaca 10200 tagttttacc ccttgcaccc atgattgagc caactgatta ttttgaatta accttgagcc 10260 aattaaacaa aatcctgacc ttttaggatt ttaagagagt aaaaatgggt tataaaggtc 10320 ttaatttggg ggattttggg aaataggtag ccaagacaat aagtacagca cacaaagtag 10380 gacacctttt acaaacagta ggcccaattt cgaaaaaaaa atgaaaagaa tttaataaag 10440 ggcagaaaca aaagagcaag agaggtgtca aaagaaaagt gttgtgggga aataaaaggg 10500 ctaagtaaaa aggcctaggc agaattggaa atttttgttc tcttttaatc ctaactttga 10560 atttccaaga aaaaccatga ttttttgtaa gccaggcccc gatacaagcc aataaagtcc 10620 ttagtgatcc accaaaggta actagagata actgtaactg agatgaaatg caaaattttg 10680 aagtgttact tgcaggttgt tatcaaattg caaacactaa actaggcact tgtgagcaga 10740 gggaaacacc agccttgtga ggaaagtaag gcaagccaaa tttgattgag ttccagatga 10800 ctaactgatt caattcttct gttgtaatgc tttcatttta agatgttgac agatgcagaa 10860 aggaccagtg aaagaaggag gaactgagcc attgatagtg ttggaatatt taagaacttg 10920 cttgagaatt tacttgtttt tggttttctt ggggacaagc aaagtttcat ttggggaatt 10980 ttgataactg ctaaataatt gtgaattaat agtagaaaat tagtcaaatt ttggcttaaa 11040 attaattatt tagcagttat ttgtgattaa aagttagaaa agcaattaag ttgaattttt 11100 ggccatagat atgaaaactg aaggtacaac aagcaaaagg cagcagaaag tgaagaaaaa 11160 gaataaaatc tgaagcagac ccagcccaac acgcgccctt agcgcgcgtc acgcgctaag 11220 cttgcaaggc agcacaggca ctaagcgagg cgttaagcac gaagatgcag gattcgttac 11280 gtgcgctaag cgcgaggcac acgctaagcg cgcgatccaa cagaagcaca cgctaagcct 11340 gcagcatgcg ctaagcgcgc ctacgaaggc ccaaagccca tttctacacc tataaataga 11400 gatccaagcc aagggagaat gtacaccttg cctcagagca cttctctcag cattccaagc 11460 ttgagctctc ccttttctct ctatattctt tgcttttatt atccattctt tctttcaccc 11520 cagttgtaaa gcccctcaat ggccatgagt ggttaatccc ctagctacgg cctggtaggc 11580 ctaaaaagcc aatgatgtat ggtgtacttc aagagttatc aatgcaaaga ggattcattc 11640 caggttttat gttctaattc tttccttttt atcttgcatt tatgtcttaa atttctgttg 11700 ggttttattc gctcgggaga gggtatttcc taataagggt ttaagaagta atgcatgcat 11760 cagttttagg ggttatacgc ttggtaaagg gtaacaccta atagaacaaa ttaagaaaag 11820 gatcgtcggg ctagcattgc taggcataga atgatggccc aatgcccatg catttagcaa 11880 catctagaat ttaaccttaa tgcattttaa ttattgaatc ttcacaaagg catttgggag 11940 ataggtagtt aaaataggct tgtcatcgtg aggcatcaag ggcaagtaaa attaatagat 12000 gtgggtagaa ctaattcaac tgcattggta atgaacatca taaattcatt catcgtaggc 12060 caattaggtt tgtccggtct tggcattttc atcaattgtc ttcctaaatt atttgatcta 12120 atagcaacaa tttattctta tgcctattcc tgtttttact atttactttt acttacaaat 12180 tgaagagtat tcaataaagt gcaataaaat ccctatggaa acgatactcg gacttccgag 12240 aattactact tagaacgatt tggtacactt gtcaaacacc tcaaca 12286 18 1802 PRT Artificial Sequence Description of Artificial Sequence plant retroelement sequence 18 Met Arg Gly Arg Thr Ala Ser Gly Asp Val Val Pro Ile Asn Leu Glu 1 5 10 15 Ile Glu Ala Thr Cys Arg Arg Asn Asn Ala Ala Arg Arg Arg Arg Glu 20 25 30 Gln Asp Ile Glu Gly Ser Ser Tyr Thr Ser Pro Pro Pro Ser Pro Asn 35 40 45 Tyr Ala Gln Met Asp Gly Glu Pro Ala Gln Arg Val Thr Leu Glu Asp 50 55 60 Phe Ser Asn Thr Thr Thr Pro Gln Phe Phe Thr Ser Ile Thr Arg Pro 65 70 75 80 Glu Val Gln Ala Asp Leu Leu Thr Gln Gly Asn Leu Phe His Gly Leu 85 90 95 Pro Asn Glu Asp Pro Tyr Ala His Leu Ala Ser Tyr Ile Glu Ile Cys 100 105 110 Ser Thr Val Lys Ile Ala Gly Val Pro Lys Asp Ala Ile Leu Leu Asn 115 120 125 Leu Phe Ser Phe Ser Leu Ala Gly Glu Ala Lys Arg Trp Leu His Ser 130 135 140 Phe Lys Gly Asn Ser Leu Arg Thr Trp Glu Glu Val Val Glu Lys Phe 145 150 155 160 Leu Lys Lys Tyr Phe Pro Glu Ser Lys Thr Val Glu Arg Lys Met Glu 165 170 175 Ile Ser Tyr Phe His Gln Phe Leu Asp Glu Ser Leu Ser Glu Ala Leu 180 185 190 Asp His Phe His Gly Leu Leu Arg Lys Thr Pro Thr His Arg Tyr Ser 195 200 205 Glu Pro Val Gln Leu Asn Ile Phe Ile Asp Asp Leu Gln Leu Leu Ile 210 215 220 Glu Thr Ala Thr Arg Gly Lys Ile Lys Leu Lys Thr Pro Glu Glu Ala 225 230 235 240 Met Glu Leu Val Glu Asn Met Ala Ala Ser Asp Gln Ala Ile Leu His 245 250 255 Asp His Thr Tyr Val Pro Thr Lys Arg Ser Leu Leu Glu Leu Ser Thr 260 265 270 Gln Asp Ala Thr Leu Val Gln Asn Lys Leu Leu Thr Arg Gln Ile Glu 275 280 285 Ala Leu Ile Glu Thr Leu Ser Lys Leu Pro Gln Gln Leu Gln Ala Ile 290 295 300 Ser Ser Ser His Ser Ser Val Leu Gln Val Glu Glu Cys Pro Thr Cys 305 310 315 320 Arg Gly Thr His Glu Pro Gly Gln Cys Ala Ser Gln Gln Asp Pro Ser 325 330 335 Arg Glu Val Asn Tyr Ile Gly Ile Leu Asn Arg Tyr Gly Phe Gln Gly 340 345 350 Tyr Asn Gln Gly Asn Pro Ser Gly Phe Asn Gln Gly Ala Thr Arg Phe 355 360 365 Asn His Glu Pro Pro Gly Phe Asn Gln Gly Arg Asn Phe Met Gln Gly 370 375 380 Ser Ser Trp Thr Asn Lys Gly Asn Gln Tyr Lys Glu Gln Arg Asn Gln 385 390 395 400 Pro Pro Tyr Gln Pro Pro Tyr Gln His Pro Ser Gln Gly Pro Asn Gln 405 410 415 Gln Glu Lys Pro Thr Lys Ile Glu Glu Leu Leu Leu Gln Phe Ile Lys 420 425 430 Glu Thr Arg Ser His Gln Lys Ser Thr Asp Ala Ala Ile Arg Asn Leu 435 440 445 Glu Val Gln Met Gly Gln Leu Ala His Asp Lys Ala Glu Arg Pro Thr 450 455 460 Arg Thr Phe Gly Ala Asn Met Glu Arg Arg Thr Pro Arg Lys Asp Lys 465 470 475 480 Ala Val Leu Thr Arg Gly Gln Arg Arg Ala Gln Glu Glu Gly Lys Val 485 490 495 Glu Gly Glu Asp Trp Pro Glu Glu Gly Arg Thr Glu Lys Thr Glu Glu 500 505 510 Glu Glu Lys Val Ala Glu Glu Pro Lys Arg Thr Lys Ser Gln Arg Ala 515 520 525 Arg Glu Ala Lys Lys Glu Glu Pro Leu Ala Leu Pro Gln Asp Leu Pro 530 535 540 Tyr Pro Met Ala Pro Thr Lys Lys Asn Lys Glu Arg Tyr Phe Ala Arg 545 550 555 560 Phe Leu Glu Ile Phe Lys Gly Leu Glu Ile Thr Met Pro Phe Gly Glu 565 570 575 Ala Leu Gln Gln Met Pro Leu Tyr Ser Lys Phe Met Lys Asp Ile Leu 580 585 590 Thr Lys Lys Gly Lys Tyr Ile Asp Asn Glu Asn Ile Val Val Gly Gly 595 600 605 Asn Cys Ser Ala Ile Ile Gln Arg Ile Leu Pro Lys Lys Phe Lys Asp 610 615 620 Pro Gly Ser Val Thr Ile Pro Cys Thr Ile Gly Lys Glu Ala Val Asn 625 630 635 640 Lys Ala Leu Ile Asp Leu Gly Ala Ser Ile Asn Leu Met Pro Leu Ser 645 650 655 Met Cys Lys Arg Ile Gly Asn Leu Lys Ile Asp Pro Thr Lys Met Thr 660 665 670 Leu Gln Leu Ala Asp Arg Ser Ile Thr Arg Pro Tyr Gly Val Val Glu 675 680 685 Asp Val Leu Val Lys Val Arg His Phe Thr Phe Pro Val Asp Phe Val 690 695 700 Ile Met Asp Ile Glu Glu Asp Thr Glu Ile Pro Leu Ile Leu Gly Arg 705 710 715 720 Pro Phe Met Leu Thr Ala Asn Cys Val Val Asp Met Gly Lys Gly Asn 725 730 735 Leu Glu Leu Thr Ile Asp Asn Gln Lys Ile Thr Phe Asp Leu Ile Lys 740 745 750 Ala Met Lys Tyr Pro Gln Glu Gly Trp Lys Cys Phe Arg Ile Glu Glu 755 760 765 Ile Asp Glu Glu Asp Val Ser Phe Leu Glu Thr Pro Lys Thr Ser Leu 770 775 780 Glu Lys Ala Met Val Asn His Leu Asp Cys Leu Thr Ser Glu Glu Glu 785 790 795 800 Glu Asp Leu Lys Ala Cys Leu Glu Asn Leu Asp Gln Glu Asp Ser Ile 805 810 815 Pro Glu Gly Glu Ala Asn Phe Glu Glu Leu Glu Lys Glu Val Pro Ser 820 825 830 Glu Lys Pro Lys Ile Glu Leu Lys Ile Leu Pro Asp His Leu Lys Tyr 835 840 845 Val Phe Leu Glu Glu Asp Lys Pro Ile Val Ile Ser Asn Ala Leu Thr 850 855 860 Thr Glu Glu Glu Asn Arg Leu Val Asp Val Leu Lys Lys His Arg Glu 865 870 875 880 Ala Ile Gly Trp His Ile Ser Asp Leu Lys Glu Ile Ser Pro Ala Tyr 885 890 895 Cys Met His Arg Ile Met Met Glu Glu Asp Tyr Lys Pro Val Arg Gln 900 905 910 Pro Gln Arg Arg Leu Asn Pro Thr Met Lys Glu Glu Val Arg Lys Glu 915 920 925 Val Leu Lys Leu Leu Glu Ala Gly Leu Ile Tyr Pro Ile Ser Asp Ser 930 935 940 Ala Trp Val Ser Pro Val Gln Val Val Pro Lys Lys Gly Gly Met Thr 945 950 955 960 Val Val Arg Asp Glu Arg Asn Asp Leu Ile Pro Thr Arg Thr Val Thr 965 970 975 Gly Trp Arg Met Cys Ile Asp Tyr Arg Lys Leu Asn Glu Ala Thr Arg 980 985 990 Lys Asp His Phe Pro Leu Pro Phe Met Asp Gln Met Leu Glu Arg Leu 995 1000 1005 Ala Gly Gln Ala Tyr Tyr Cys Phe Leu Asp Gly Tyr Ser Gly Tyr Asn 1010 1015 1020 Gln Ile Ala Val Asp Pro Arg Asp Gln Glu Lys Thr Ala Phe Thr Cys 1025 1030 1035 1040 Pro Phe Gly Val Phe Ala Tyr Arg Arg Met Pro Phe Gly Leu Cys Asn 1045 1050 1055 Ala Pro Ala Thr Phe Gln Arg Cys Met Leu Ala Ile Phe Ser Asp Met 1060 1065 1070 Val Glu Lys Ser Ile Glu Val Phe Met Asp Asp Phe Ser Val Phe Gly 1075 1080 1085 Pro Ser Phe Asp Ser Cys Leu Arg Asn Leu Glu Arg Val Leu Gln Arg 1090 1095 1100 Cys Glu Glu Thr Asn Leu Val Leu Asn Trp Glu Lys Cys His Phe Met 1105 1110 1115 1120 Val Arg Glu Gly Ile Val Leu Gly His Lys Ile Ser Ala Arg Gly Ile 1125 1130 1135 Glu Val Asp Arg Ala Lys Ile Asp Val Ile Glu Lys Leu Pro Pro Pro 1140 1145 1150 Leu Asn Val Lys Gly Val Arg Ser Phe Leu Gly His Ala Gly Phe Tyr 1155 1160 1165 Arg Arg Phe Ile Lys Asp Phe Ser Lys Ile Ala Arg Pro Leu Ser Asn 1170 1175 1180 Leu Leu Asn Lys Asp Val Ala Phe Val Phe Asp Glu Glu Cys Leu Ala 1185 1190 1195 1200 Ala Phe Gln Ser Leu Lys Asn Lys Leu Val Thr Ala Pro Val Met Ile 1205 1210 1215 Ala Pro Asp Trp Asn Lys Asp Phe Glu Leu Met Cys Asp Ala Ser Asp 1220 1225 1230 Tyr Ala Val Gly Ala Val Leu Gly Gln Arg Lys Asp Lys Val Phe His 1235 1240 1245 Ala Ile Tyr Tyr Ala Ser Lys Val Leu Asn Glu Ala Gln Leu Asn Tyr 1250 1255 1260 Ala Thr Thr Glu Lys Glu Met Leu Ala Ile Val Phe Ala Leu Glu Lys 1265 1270 1275 1280 Phe Arg Ser Tyr Leu Ile Gly Ser Arg Val Ile Ile Tyr Thr Asp His 1285 1290 1295 Ala Ala Ile Lys His Leu Leu Ala Lys Thr Asp Ser Lys Pro Arg Leu 1300 1305 1310 Ile Arg Trp Val Leu Leu Leu Gln Glu Phe Asp Ile Ile Ile Lys Asp 1315 1320 1325 Lys Lys Gly Ser Glu Asn Val Val Ala Asn His Leu Ser Arg Leu Lys 1330 1335 1340 Asn Glu Glu Val Thr Lys Glu Glu Pro Glu Val Lys Gly Glu Phe Pro 1345 1350 1355 1360 Asp Glu Phe Leu Leu Gln Val Thr Glu Arg Pro Trp Phe Ala Asp Met 1365 1370 1375 Ala Asn Tyr Lys Ala Thr Gly Val Ile Pro Glu Glu Phe Asn Trp Ser 1380 1385 1390 Gln Arg Lys Lys Phe Leu His Asp Ala Arg Phe Tyr Val Trp Asp Asp 1395 1400 1405 Pro His Leu Phe Lys Ala Gly Ala Asp Asn Leu Leu Arg Arg Cys Val 1410 1415 1420 Thr Lys Glu Glu Ala Arg Ser Ile Leu Trp His Cys His Ser Ser Pro 1425 1430 1435 1440 Tyr Gly Gly His His Ser Gly Asp Arg Thr Ala Ala Lys Val Leu Gln 1445 1450 1455 Ser Gly Phe Phe Trp Pro Ser Ile Phe Lys Asp Ala His Glu Phe Val 1460 1465 1470 Arg Cys Cys Asp Lys Cys Gln Arg Thr Gly Gly Ile Ser Arg Arg Asn 1475 1480 1485 Glu Met Pro Leu Gln Asn Ile Met Glu Val Glu Ile Phe Asp Cys Trp 1490 1495 1500 Gly Ile Asp Phe Met Gly Pro Phe Pro Ser Ser Tyr Gly Asn Val Tyr 1505 1510 1515 1520 Ile Leu Val Ala Val Asp Tyr Val Ser Lys Trp Val Glu Ala Ile Ala 1525 1530 1535 Thr Pro Lys Asp Asp Ala Arg Val Val Ile Lys Phe Leu Lys Lys Asn 1540 1545 1550 Ile Phe Ser Arg Phe Gly Val Pro Arg Ala Leu Ile Ser Asp Arg Gly 1555 1560 1565 Thr His Phe Cys Asn Asn Gln Leu Lys Lys Val Leu Glu His Tyr Asn 1570 1575 1580 Val Arg His Lys Val Ala Thr Pro Tyr His Pro Gln Thr Asn Gly Gln 1585 1590 1595 1600 Ala Glu Ile Ser Asn Arg Glu Leu Lys Arg Ile Leu Glu Lys Thr Val 1605 1610 1615 Ala Ser Thr Arg Lys Asp Trp Ser Leu Lys Leu Asp Asp Ala Leu Trp 1620 1625 1630 Ala Tyr Arg Thr Ala Phe Lys Thr Pro Ile Gly Leu Ser Pro Phe Gln 1635 1640 1645 Leu Val Tyr Gly Lys Ala Cys His Leu Pro Val Glu Leu Glu Tyr Lys 1650 1655 1660 Ala Tyr Trp Ala Leu Lys Leu Leu Asn Phe Asp Asn Asn Ala Cys Gly 1665 1670 1675 1680 Glu Lys Arg Lys Leu Gln Leu Leu Glu Leu Glu Glu Met Arg Leu Asn 1685 1690 1695 Ala Tyr Glu Ser Ser Lys Ile Tyr Lys Glu Lys Met Lys Ala Tyr His 1700 1705 1710 Asp Lys Lys Leu Leu Arg Lys Glu Phe Gln Pro Gly Gln Gln Val Leu 1715 1720 1725 Leu Phe Asn Ser Arg Leu Arg Leu Phe Pro Gly Lys Leu Lys Ser Lys 1730 1735 1740 Trp Ser Gly Pro Phe Ile Ile Lys Glu Val Arg Pro Tyr Gly Ala Val 1745 1750 1755 1760 Glu Leu Val Asp Pro Arg Glu Glu Asp Phe Glu Lys Lys Trp Ile Val 1765 1770 1775 Asn Gly Gln Arg Leu Lys Pro Tyr Asn Gly Gly Gln Leu Glu Arg Leu 1780 1785 1790 Thr Thr Ile Ile Tyr Leu Asn Asp Pro Glx 1795 1800 19 9829 DNA Glycine max 19 tgataactgc taaataattg tgaattaata gtagaaaatt agtcaaattt tggcttaaaa 60 ttaattattt agcagttatt tgtgattaaa agttagaaaa gcaattaagt tgaatttttg 120 gccatagata tgaaaactga aggtacaaca agcaaaaggc agcagaaagt gaagaaaaag 180 aataaaatct gaagcagacc cagcccaaca cgcgccctta gcgcgcgtca cgcgctaagc 240 ttgcaaggca gcacaggcac taagcgaggc gttaagcacg aagatgcagg attcgttacg 300 tgcgctaagc gcgaggcaca cgctaagcgc gcgatccaac agaagcacac gctaagcctg 360 cagcatgcgc taagcgcgcc tacgaaggcc caaagcccat ttctacacct ataaatagag 420 atccaagcca agggagaatg tacaccttgc ctcagagcac ttctctcagc attccaagct 480 tgagctctcc cttttctctc tatattcttt gcttttatta tccattcttt ctttcacccc 540 agttgtaaag cccctcaatg gccatgagtg gttaatcccc tagctacggc ctggtaggcc 600 taaaaagcca atgatgtatg gtgtacttca agagttatca atgcaaagag gattcattcc 660 aggttttatg ttctaattct ttccttttta tcttgcattt atgtcttaaa tttctgttgg 720 gttttattcg ctcgggagag ggtatttcct aataagggtt taagaagtaa tgcatgcatc 780 agttttaggg gttatacgct tggtaaaggg taacacctaa tagaacaaat taagaaaagg 840 atcgtcgggc tagcattgct aggcatagaa tgatggccca atgcccatgc atttagcaac 900 atctagaatt taaccttaat gcattttaat tattgaatct tcacaaaggc atttgggaga 960 taggtagtta aaataggctt gtcatcgtga ggcatcaagg gcaagtaaaa ttaatagatg 1020 tgggtagaac taattcaact gcattggtaa tgaacatcat aaattcattc atcgtaggcc 1080 aattaggttt gtccggtctt ggcattttca tcaattgtct tcctaaatta tttgatctaa 1140 tagcaacaat ttattcttat gcctattcct gtttttacta tttactttta cttacaaatt 1200 gaagagtatt caataaagtg caataaaatc cctatggaaa cgatactcgg acttccgaga 1260 attactactt agaacgattt ggtacacttg tcaaacacct caacaagttt ttggcgccgt 1320 tgtcggggat tttgttctcg cacttaattg ccatactata ttagtttgta agcttaattc 1380 ttcttttctt ggctcattct tttattattc tttactttac tttttcttct atcctttctt 1440 tcttctccca taaattgcac gggtagtgcc tttttgtttt tatacgaggt agaactgcat 1500 ctggagacgt tgttcctatt aacttagaaa ttgaagctac gtgtcggcgt aacaacgctg 1560 caagaagaag aagggagcaa gacatagaag gaagtagtta cacctcacct cctccttctc 1620 caaattatgc tcagatggac ggggaaccgg cacaaagagt cacactagag gacttctcta 1680 ataccaccac tcctcagttc tttacaagta tcacaaggcc ggaagtccaa gcagatctcc 1740 tactcaaggg aacctcttcc atggtcttcc aaatgaagat ccatatgcgc atctagcctc 1800 atacatagag atatgcagca ccgttaaaat cgccggagtt ccaaaagatg cgatactcct 1860 taacctcttt tccttttccc tagcaggaga ggcaaaaaga tggttgcact cctttaaagg 1920 caatagctta agaacatggg aagaagtagt ggaaaaattc ttaaagaagt atttcccaga 1980 gtcaaagacc gtcgaacgaa agatggagat ttcttatttc catcaatttc tggatgaatc 2040 ccttagcgaa gcactagacc atttccacgg attgctaaga aaaacaccaa cacacagata 2100 cagcgagcca gtacaactaa acatattcat cgatgacttg caaccttaat cgaaacagct 2160 actagaggga agatcaagct gaagactccc gaagaagcga tggagctcgt cgagaacatg 2220 gcggctagcg atcaagcaat ccttcatgat cacacttatg ttcccacaaa aagaagcctc 2280 ttggagctta gcacgcagga cgcaactttg gtacaaaaca agctgttgac gaggcagata 2340 gaagccctca tcgaaaccct cagcaagctg cctcaacaat tacaagcgat aagttcttcc 2400 cactcttctg ttttgcaggt agaagaatgc cccacatgca gagggacaca tgagcctgga 2460 caatgtgcaa gccaacaaga cccctctcgt gaagtaaatt atataggcat actaaatcgt 2520 tacggatttc agggctacaa ccagggaaat ccatctggat tcaatcaagg ggcaacaaga 2580 tttaatcacg agccaccggg gtttaatcaa ggaagaaact tcatgcaagg ctcaagttgg 2640 acgaataaag gaaatcaata taaggagcaa aggaaccaac caccatacca gccaccatac 2700 cagcacccta gccaaggtcc gaatcagcaa gaaaagccca ccaaaataga ggaactgctg 2760 ctgcaattca tcaaggagac aagatcacat caaaagagca cggatgcagc cattcggaat 2820 ctagaagttc aaatgggcca actggcgcat gacaaagccg aacggcccac tagaactttc 2880 ggtgctaaca tggagaagaa ccccaaggaa gaatgaaaag cagtactgac ttgagggcag 2940 agaagagcgc aggaggaggg taaggttgaa ggagaagact ggccagaaga aggaaggaca 3000 gagaagacag aagaagaaga gaaggtggca tcaccaccta agaccaagag ccagagagca 3060 agggaagcca agaaggaaga accactagcc cttccacagg atctcccata tcttatggca 3120 cccaccaaga agaacaagga gcgttacttt agacgtttct tggaaatatt caaagggtta 3180 gaaatcacta tgccattcgg ggaagcctta cagcagatgc ccctctactc caaatttatg 3240 aaagacatcc tcaccaagaa ggggaagtat attgacaacg agaatattgt ggtaggaggc 3300 aattgcagtg cgataataca aaggaagcta cccaagaagt ttaaagaccc cggaagtgtt 3360 accatcccgt gcaccattgg gaaggaagcc gtaaacaagg ccctcattga tctaagagca 3420 agtatcaatc tgatgccctt gtcaatgtgc aaaagaattg ggaatttgaa gatagatccc 3480 accaagatga cgcttcaact ggcagaccgc tcaatcacaa ggccatatgg ggtggtagaa 3540 gatgtcctgg tcaaggtacg ccacttcact tttccggtgg acttttttat catggatatc 3600 gaagaagaca ctgagattcc ccttatctta ggcagaccct tcatgctgac tgccaactgt 3660 gtggtggata tggggaatgg gaacttagag ttgactattg ataatcagaa gatcaccttt 3720 gaccttatca aggcaatgaa gtacccacag gagggttgga agtgcttcag aatagaggag 3780 attgatgagg aagatgtcag ttttctcgag acaccataga cttcgctaga aaaagcaatg 3840 gtaaatgctt tagactgtct aaccagtgaa gaggaagaag atctgaaggc ttgcttggaa 3900 aacttggatc aagaagacag tattcctgag ggagaagcca atttcgagac gctagagaag 3960 gaagttccgt ctgagaagaa gaagatagag ttgaagatat tgcctaatca tttgaagtat 4020 gtgttcttgg aggaagataa gcctatagtg atcagtaatg cactcacaac agaggaagaa 4080 aataggttgg tagacgtcct aaagaaacac agggaagcaa ttggatggca catatcggat 4140 ctcaggaatt agccctgcct actgcatgca catgataatg atggaagagg actacaagcc 4200 agtccgacaa ccctagaggc ggctgaatcc aacaatgaag gaagaggtaa gaaaggaggt 4260 gctcaagctt ttggaggctg ggttcatata ccccatctct gatagcgctt gggtaagtcc 4320 agtacaggtg gttcctaaga aaggcggaat gacagtggta cgaaatgaga ggaatgactt 4380 gataccaaca cgaactgcca ctggttggtg gatgtgtatc gactatcgca agttgaatga 4440 agccacacag aaggaccatt tccccttacc tttcatggat tagatgctgg aaaggcttgc 4500 agggcaggca tactactgct tttggatgga tattcaggat acaaccagat cgcggtagac 4560 cccagagatc aggagaagac ggcctttaca tgccccttcg gcgtctttgc ttacagaagg 4620 atgtcattcg ggttatgtaa cgcactagcc atatttcaga ggtgcatgct agccattttt 4680 tcagacatgg tggagaagag catcgaggta tttatggacg acttctggat ttttggaccc 4740 tcatttgaca actatttgag gaacctagag atggtactac agaggtgcgt atagactaac 4800 ttggtactaa attgggaaaa gtgtcatttc atggttcgag agggcatagt cctgagccac 4860 aagatctcag ccagagggat tgaggttgat cagacaaaga tagacgtcat tgagaagttg 4920 ccgccaccaa tgaatgttaa aggtgtcaga agtttcttag ggcatgcagg tttctacagg 4980 aggtccatca aggacttctc gaagattgcc aggcccttaa gcaatctgtt gaataaggat 5040 gtggctttta agtttgatga agaatgttca gcagcatttt tagacactaa agaataagct 5100 caccactgca ccagtaatga ttgcaccaga ctggaataaa gattttgaac taatgtgtga 5160 tgccagtgat tatgcagtag gagcagtttt gggacagagg cacgacaagg tatttcacgc 5220 catctattat gctagtaagg tccttaataa agcataacta aattatgcga ccacagaaaa 5280 gcagatgcta gccattgtct tttccttgga gaagttcagg tcgtacttga tagggtcgag 5340 ggtcaccatt ttcacaaatc atgctgccat caagcacttg ctcgccaaaa cagactcaaa 5400 gctgaggttg attagatggg tcctgctgat acaagaattt gacatcatca tcaaggacaa 5460 taaaggatcc aagaatgtgg tagccaatca tttatcctga ttaaagaatg aagaagtcac 5520 caaggaagaa ccagaggtaa aaggagaatt tcctgatgaa tttcttttgt aggttaccac 5580 cagaccttgg tttgcagaga tggctaacta caaagccaca ggagtcattc cagaggagtt 5640 taattggagt cagaggaaga aattcttgca tgatgcacgc ttctatgtgt gggataatcc 5700 tcatttgttt agggcaggag ctgataatct attaaggaga tgcgtcacaa aggaggaagc 5760 acagagcatt ctttggcact gccacagttc accctatggc ggacaccaca gtggggacag 5820 aacagcagca aaagtgctac aatcaggttt tttctggcct tctattttta aagatgctta 5880 cgagtttgtg cgttgttgtg ataaatgcca gagaacaggg gggatatctc gaaggatgga 5940 gatgcctttg cagaatatca tggaagtaga gatctttgac tgttggggca tagacttcat 6000 ggggcctctt ccttcttcat acgagaatgt ttacatcctg gtagctgtgg attacgtctc 6060 caaatgggtg gaggccatag ccattccaaa agacgatgcc agggtagtga taaaatttct 6120 gaagaagaac atcttttccc attttggagt cccatgagcc ttgattagtg atggggaacg 6180 cacttctgca ataatcagtt gaagaaagtc ctggagcact ataatgtaag acataaggtg 6240 gccacacctt atcaccctca gacaaatggc caagtagaaa tttctaacaa agagctcaag 6300 cgaatcctgg agaagacagt tgcatcatca agaaagaatt gggccttgaa gctcgatgat 6360 actctttggg cctacagggc agcattcaaa actcccatcg gcttatcacc gtttcagcta 6420 gtgtatggga aggcatgtca tttaccagtg gagctggagc acaaagcata ttaggctctc 6480 gagttactca actttgataa caacgcatgc ggagaaaaga ggaagctaca gttgctggaa 6540 ttagaagaga tgagactgaa tgcctacgag tcatccaaaa tttacaacca aaagatgaag 6600 gcatatcatg acaagaagct acagaggaaa gaattccaac catggcagca ggtattactc 6660 tttaaatcaa ggctaaggct attcccaggt aagctgaagt ccaagtggtt agggccgttc 6720 ataatcaatg aagtcagacc tcacggagca gtagaattgg gggaccctag agaagagaac 6780 tttgagaaga aatggatcgt caatggacaa cgcttaaagc tttataacga aggacaacta 6840 gagcgattga cgaccatcat ctacttgaat gacccttgag gaggcctagt gtctagctaa 6900 agacaataaa ctaagcgctg gttgggaggc aacccaacat attttgtaaa aatgtagtca 6960 tttttctgta ttccttcaaa aaaaaaggga aaagcccaat aggtgcaaat agaaaacagc 7020 aggtgcagaa agtaaagacc cagtaggtga agtcagcaat aggaggggtg ccaatagaag 7080 aagcgaagtg ggctgcacga agccacgcgc atctaggcgc taagcgccta ggtatatttt 7140 caatttttaa attttaaaaa ttctgaggga aaccaaggga cgcttccctt ggtatgctta 7200 gcgaccagat gcgcgctaag cgcgcgaacc ataaattgct ggacagtttt caaaactgtc 7260 ccacccctca gctgcccttt tgtattttaa atttcaacca cctcattttt ttttctcttc 7320 tgcgcactcc cactccctat accctttttc tctacatttc ctctaaactt actcgcctcc 7380 ctgtgcctct tcacgtagtt tttacgaaaa taggtgagat tgggaatctg gactgttgct 7440 gtaatacttt gcaggtacca tcacgctaag ccctacacaa aggcttagcg agaaaaagaa 7500 acatagaaag gaagaaagaa gcatgcgcta agcctgcgcc agacaggaca agaaaacaca 7560 gcatgcgttt agccggcacc tcgtgctaag cgcgctcatg agactcagtg aacgcgctaa 7620 gcatggggct gggccttagg gcccatcagc cctcgtgcct tactttctgc accctctttt 7680 tcactaacta cactcccttc tgaatttctt tttgcaccct cctctattac taaccacaat 7740 ctatttttcc gtctttgttt ctttgttttt tcagatggcc tcccgcaaac gccgagctgt 7800 gcccacacct ggggaagcat caagctggga ctcttcccgc ttcacctcgg agatcatttg 7860 gcatagatac caggataaca ttcagctccg gaacattctt ctggagagga atgtcgagct 7920 cacacccagg atgtttgatg agttcctcca ggagctccag aggtgcagat gggaccaggt 7980 gttaacccga cttccagaga agaggattga tgtcgctctg gtgaaggagt tttactccaa 8040 cttatatgat ccagaggacc atagtccaaa gttttgtagg gttcaaggac aggtcatgtg 8100 gtttgatgca gagacgatta acgacttcct tgacacccca gtcatcctgg cagatgtaga 8160 ggagtaccca gcctactctc agtacctccg cactcctccc gatcatgatg ccatcctctc 8220 cactttgtgt actccagggg gacggtttgt tctgaatgtt gatggtgccc cctagaagtt 8280 gctgcggaag gatctgacga cactcgctca gacatagagt gtcctttctt attttaacct 8340 tgttcttact tctcacactt ctgatattaa tgttgacagg gcccgtctca tatatggctt 8400 ggtgatgaag atggacctgg acgtggacag ttttatttcc cagcaaatca gtcagatcgc 8460 ccaatccaac acatccaggc tcgggttccc agcgttgatc acggcactgt gtgacattca 8520 gggggttgtt tctaacaccc tgatttttga gttactcaat cctatgatta accttgcgta 8580 cattacacta ctaaaaaaaa gctattttac gacgcgcgtt ccacatcgtt tctgccaaaa 8640 atgtcgtaat aggagtagcg gtggcaattc cgtaaataag tgagcatttt atgtgccatg 8700 tgcatggcgc gtgacacatt caacgacgtt ggccatgggt gcccgtcttt gtaggtggcg 8760 cgctggtaac ttaagacggt gcacttaaaa acatcgtcgt tgaaattttg aatttcgaag 8820 acgttgctct taagccaccg tcgttaaggt tgatgtatat aatgttgtaa tttgcgctat 8880 ttcgtgaaca ctcgctcgag ctcccgcttc cctgtgtgtc tgaaatttct gtgtactgtg 8940 acctcgccat gacttgtggc gtttgcccac acccccgtca cctcgtccgg catctcgtct 9000 tgtggtggca ccgccgaagc cagtgagtac ccctttttgg aggggtcgta acacggctgt 9060 gttttgaagg taaggttgtg cgaagatttg atgctccata gttgttactt gctctgagtt 9120 tttcttttag tgatgtatct tttacccctc tttcagtgct tcttccctca gaatttgatt 9180 gccggtatta gaaccccact attcatcagg tccaaacaag cttaaatcat ggtaaatgta 9240 cttcttgaca aatccaacat ttgcaaggtg gtttgacata tgagaaatag ctttaaccta 9300 atgttcttaa atttattatg aagctctcta gcgattacga aaatctctca atatcttctc 9360 tctctgtctc acatgcatca ctgtaagata ggtgtcaaaa agaaaggatt gaagttaaat 9420 ttaaacctaa tgttttgaaa tgaaggaaaa aaagaaagag attaatgacg ctagggaact 9480 tgaatgaaga aagagaaagg aacataatta gtcctttgaa ctgattgggg tggggagtgt 9540 ggcacgaaac ataatttcta gttctatgga tttattcgtg acactgtggt aggaccaagc 9600 aaactctgcc cccagagtgc gcagtgtctt gcagtctgag aggttctttt gttgggctag 9660 tttgaggaat tcttcattgc agggttgagc acggtggcca atggccaagg agagaaaaga 9720 cagtactgtc aaaatggtta atggtaagat gagtgaagat gacatgtttt tttgttgtct 9780 ctttgtgtgt ttccttttgg tgggaaaatg tgatgcatag agagatcga 9829 20 12571 DNA Glycine max 20 gatcttaaat tcttaaactt tgataacagt gcatacggag agaagagaaa gttgcagtta 60 ctggaactcg aagaaatgag gttgaacgct tacgaatcat ctaggattta caagcagaag 120 gtaaaggcgt atcatgataa gaaattacaa aagaaagaat tccagccagg gcagcaagta 180 ctactcttca actccaggtt gagattattc acaggaaagc tgaagtcaaa gtggtcagga 240 tcgttcatta ttaaggaaat cagacctcac ggagcggtag aattggtgga ccctcgagaa 300 gaaaattatg agaagaaatg gatcgtcaac ggacaacgct taaaaattta caatggagga 360 caactagaga agttgacgac catcatgcat ttaaaagatt cttgaaagaa gccctatgtc 420 tagctaaaga cattaaacta agcgctggtt gggaggcaac ccaacatact tatgtaaggt 480 atttataagt atttatattc tgtctttatt atattttgca gttgttattt caggttaaaa 540 gaaaaaacag gggccctccg gactcgcacc agagtatcaa cgtccatatc tgaggcaccc 600 cctacttctc agccttccgc tccatcacct actgatcttc atgctcagat gttgcggtct 660 attcacacag gacaggagac ccttatggag aacatgcaca agctgtcctt tcatctacat 720 atggatccac cactgatcac tccataggtc tatcgtcagc gggtcgtctg gccatgagac 780 cagctctcca ctgacagggg ggaagagccc tctggagatg ctgcagttga tgaagacctc 840 atagcagact tggctagtgc tgattggggt ccatgggcag atttgggagg cggcacagga 900 cactggtttt atttttcttg atgtttttgt ttatgtttaa tgtttatgtt ttatgtcttt 960 atgttttatt tggtttctag ttattatggt cttaattgta gttttatgtt caaaatgaaa 1020 agcagtggta ataatattag atttgagcat atgcgtgaat aaataaattg catgataact 1080 tgagaaatga caattttgag tttgttctaa aaggtccaac actggaaagg ctactagtca 1140 ttggaaagca ctggtcttgg aagcaaaagt caaatcaagg aatgaaacat gattcacgga 1200 aaaggaaagg ttagcttgat ggaatgaaga cacatctggt acgccaatac tgaattaatc 1260 ccggtgagag tgtgacctta attgtgagag aaaacgcctg tttttaagct cttagttttg 1320 catcattctt ggactgttaa aattagttac ttaaggtgga tatgatcaag gccatgtttg 1380 ttttatttta cccactcagc caaaaagcca acccaacata attttatccc ttgcacccat 1440 attgagccaa aaagaattat aatgatttat ttgagtaaac ccctgagcca agaaattgat 1500 attcctaacc ttgtgtagga ttctaagaga gcagtagggt tccaaatgct tataaggcct 1560 tattttgggg gattttgaac aaatgggtaa agtagccaag gtaataacac acattagaac 1620 acctctaaat aattgtgagc ccattactat tattattatt attattatta ttattattat 1680 tattattatt attattatta ttattattat tattggttat aaaaaaaaga agaaaaaaag 1740 agaaagaata agaagagaaa gggcaaagaa aaaaaatgaa aaagagaggt ttcagtggaa 1800 agtgctgaag gcaaaaaagg ctaagtggga aataggtctt ggcaagacct taaatttttg 1860 gaatgtatgc tctcttataa ccttatattt tgaatttcca agaaaaacca tgattctttg 1920 ttagccaggc cccattacaa ggcatgaaag tccttagtga cccaccgaag gtaattaagg 1980 ctaaccttaa ccaagatgaa gtacaaaact cttgagtttt atttacaggt tgttaaaatt 2040 gcaaacactt gaccaggcac ttgtgagtag agagaaacac cagttttgta aggaagtaag 2100 gcaagccgga cctgttggaa ttccatataa ttgacttgtt tctgctcttg tgtttatgct 2160 tttatttcaa gatcatgaca gatgcaaaga gaccagccaa aggatcaagg aattgaagtc 2220 atggagagtg ttggaatgat tggaacttgc ttgagaaaat ttttgcttaa gaatggaata 2280 attttattct ttttatttgc ttggggacaa gcaaagttta atttggggga ttttgataac 2340 tgctaaataa tagtgaatta atagtggaaa attggtctga aattaactta gaattaatta 2400 tttagtagtt atttatgctt taatttggaa agatttaatt aattttgaat tctgattgca 2460 gatgtgaaaa agggaggtac aacaagcaaa aaggagcaaa aataaagaaa aagaagaaga 2520 aaatcagacg aagacccaag cccaaatttt cacctataaa taagaaggtc agcctagcaa 2580 aacacacaca ctttcagaga gctcagtttt cagacttctg gcactcagtt ctctccttct 2640 ccttcccttt ttcttatatt cttattacct ttctttcacc cccttctcat tgtaaagccc 2700 tcttgactat gagtggctaa acccctagct agggcctggc aggcctaaaa agccaatgat 2760 gtatggagca tttcaagagt tatcaataaa gagaggattt ccttccaggt tctttattta 2820 ccgttctttc ttatttatcc tgtatttcgg accttatttt ctgttagggt ttagtccact 2880 cgggagaggg taaagcctaa ttaggggtaa ggaatgaata cttgaatcta ttttaagggt 2940 tagtccattc gggagagggt aaagcttaat agaacaataa aaggaagaaa ttatcgggtt 3000 atcattagag ggttttcctt ccaggttctt ttatctgctt ttctttctta ttctgcatct 3060 cagtctttat tttctgttag tctttagtcc actcgggaga gggtaaagcc taattaaggg 3120 taaggaatga ttgcgtgaat ctgttttaag ggttagttca ctcaggagag ggtaacgctt 3180 aatagaacaa taaaagaaaa aaatcacagg gttagcattg acccgatgcc catactttag 3240 caaacatata gaatttaatc ttaatgcatc ttagttattg agtctttgca aagggcattt 3300 ggaagatagg taattaaggt aggcttgtca tcatgaggca tcaggggcaa gtagatggat 3360 agatgtgggg cagaatcagt tcactggtat tgataacaga caaatcttga atccatatat 3420 ctaggctgat tagacttttt aggttttagc aattttatta tatagatttt attccctatt 3480 ttattgtttg aagtttctta ttctattgtt gggttttctt agaagtagct attccttatt 3540 ttactgttgg gttttcttag aaatagttat tccttattgt tgggtttctt agaagtagtt 3600 attccttatt ttactgttgg gttttattag gagtacttat cccctgttta ggagtaggta 3660 tttaggctta ttagatttag taatatttta tagactttat tctttattta ttgcttgagt 3720 ttcctttaat ttagaagtag ctgcttagat ttaaattact ttatctttat cctttaatct 3780 tatctttaaa tcttttatct tttccttatc ttatctttta tctttcttta tcttttattt 3840 caaatttctt atcccttgct agatttaaat tgcatttaat tttatacact aaatttacaa 3900 tttgcaaact aaaaagtact tcacataagt gcaacaaaat ccctatggta cgatactcga 3960 cttaccgaga gattattact acgagcgatt tggtacactt gccaaagagc taacaaagat 4020 attgcctgat catctaaagt atgtgttctt ggaggaagat aaacctatag taatcagtaa 4080 cgcactcaca acaaaggagg aaaataggtt ggttgatgtc ctcaagaaat acagggaagc 4140 aattggatgg catatatcgg atctcaagga aattagccct gcttactaca tgcacagaat 4200 aatgatggaa gagaactaca agccagtccg acaaccccag aggcggctga atccaacaat 4260 gaaggaagag gtaagaaagg aggtactcaa gctcttggag gctgggctca tatacccctt 4320 ctctaacagt gcttgggtaa gcccagtaca ggtggttccc aagaaaggtg aaatgacagt 4380 ggtacgaaat gagaagaatg acttgatacc cagacgaact atcactggtt ggcgaatgtg 4440 tatcaactat cgcaagctga atgaagccac acgaaaggac catttcccct tacttttcat 4500 ggatcagatg ctagagagac ttgtagggca ggcatactac tatttcttgg atggatactc 4560 gggatataat cagatcgcgg tggaccccag agatcaagag aaggcggcct ttacatgccc 4620 ttttggcgtt tttgcttata gaaggatgcc attcgggtta tgtaatgcac cagccacatt 4680 tcagaggttc atgctggcca ttttttcaga catggtgtag aaaagcattg aggtatttat 4740 ggacgacttc tgggtttttg gaccctcatt taacagtttg aggaacctag agatggtact 4800 ttagagttga gtagagacta acttggtact gaactgggag aagtgtcact tcatggttca 4860 agagggcatc gtcctaggcc acaagatctc agcaagaggg attgaggtcg atcgggcaaa 4920 gatagacgtc atcgagaagc tgccaccacc actgaatgtt aaaggggtta gaagtttctt 4980 agggcatgca ggtttctaca agaggtttat caaggacttc tcaaagattg ccaggcccct 5040 aagtaacctg ttgaataaag acatggtttt caagtttgat gaagaatgtt caacagcatt 5100 ccaatcattg aagaataagc ttaccactgc acctgtaatg attgcacccg actggaataa 5160 agattttgaa ctaatgtgtg atgccaatga ttatgcagta ggagcagttc tgggatagag 5220 gcacgacaag gtatttcacg ccatctatta tgctagcaag gtcctgaatg aagcatagtt 5280 gaattatgca accatagaaa aggagatgct agccattgtc tttgccttgg agaaattcaa 5340 gtcatacttg atagggttga gggtcaccat tttcacagat catgctgcca tcaagcacct 5400 gcttgccata acagactcaa aaccgaggtt gattagatgg gtcctactgt tacaagaatt 5460 tgacatcatc atcaaggaca agaaaggatc cgagaatgtg gtagccaatc atctatctcg 5520 attgaagaat gaagaagtca ccaaggaaga accagaggta aaaggtgaat ttcctgatga 5580 gtttcttttg caggttaccg ctagatcttg gtttgcagac atggccaatt acaaagccac 5640 gggagtcatt ccagaggagc ttaattggag tcaaaggaag aaattcttgc acaatgcacg 5700 cttctatgtg tgggatgatc ctcatctgtt caaggcagga gcagataatt tactaaggag 5760 atgcgtcaca aaggaggaag cacggagcat tctttggcac tgccacagtt caccctatgg 5820 cggtcaccac agtggggaca gaacagcagc aaaagtgcta caatcaggtt ttttctggcc 5880 ctctattttt aaagatgctc acgagtttgt gcgttgttgt gataaatgcc aaagaacagg 5940 ggggatatct cgaagaaatg agatgccttt gcaaaatatc atggaagtag agatctttga 6000 ctgttggggc atagacttca tcgggcccct gccttcgtta tatggaaatg tctacatctt 6060 ggtagttgtg gattacgtct ccaaatgggt ggaagtcata gctacgccaa aggatgatgc 6120 caaggtagta atcaaatttc tgaagaagaa cattttttcc cgttttggag tcccacgagc 6180 cttgattagt gataggggaa cgcacttctg caacaatcag ttgaagaaag tcttggagca 6240 ctataatgtc cgacataagg tggccacacc ttatcatcct cagacaaatg gccaagcaga 6300 aatctctaac agggagctca aggcgaatct tggaaaagac aattgcatca tcaagaaagg 6360 attgggcctt gaagctcgat gatactctct tggcctatag ggcagcgttc aagactctca 6420 tcggcttatc gccatttcag ctagtgtatg ggaaggcatg ccatttacca gtggagctag 6480 agcacaaagc atattgggct ctcaagttgc tcaacttcga caacaacgca tgcggggaaa 6540 agaggaagct acagatgttg gaattagaag agatgagact gaatgcctac gagtcatcca 6600 gaatttacaa gcaaaagatg aaggcatatc atgataaaaa gctacagagg aaagaattcc 6660 atccagggaa gcaggtatta ctctttaact cgaggctaag gctattccca ggtaagctga 6720 agtccaagtg gtcaaggcca tttatcataa aagaagtcag acctcatgga gcagtagaat 6780 tggtggaccc ttgagaagag aactttaaga agaaatggat cgtcaatcga cagcgcttga 6840 agccctacaa cggaggacaa ctcgagcgat tgacgaccat catctactta aatgatcctt 6900 gagaaggcct actgtctagc taaagacaat aaactaagca ctggttggga ggcaacccaa 6960 catatttttg taaaaatgta gttattttta ttttatgtaa aaaaaaacaa gagggcccaa 7020 taggtgcaaa tagcaaacag gaggtgcaaa aagcaaaggc ccaacaggtg aagacaacaa 7080 taggaagggt gccaatagca aaactgaagt gggctgcatg aagccgcgcg ctaagcgccc 7140 aggtatgttt ttaaaatctg atgggcaacc aagggacgct ttccttggtg cgcttagcgg 7200 ccacatgcgc gctaagcgcg taagtcataa attactggac agttttcgaa actgcccaac 7260 ccctcagctg cctcctccgc gttattaaat tacaaccatt tcatttcatt atccttcttt 7320 tctttcgcaa atctaccctt ctttgcacct ctgctactgt aacccctgaa ttcttggtct 7380 tttcacacaa aacaatcact aacgaaggta aagaattgct ttgtatggat gttgttatga 7440 atgcacaggt aacagcacgc taagccctgc tcgacgctta gccaatgaag acggattgaa 7500 ggccataacg acgagctcgt taagcgtgac gaagcacgct aagcaggcgc ctgacaggac 7560 gagaaagcaa agcgcgcgct tagccggcac ttccgcgcta agcgcgctca tgaacatcac 7620 tgaacgcgct aaacgtgtgc cagaggcgct aaacgcgtgc cagaggcgct aaacgcgtgc 7680 attagtcaca gcaggatggt gctaagcgcg gggttgggcc tcagggccca tcaaccctcg 7740 caccttactt gttgcacccc tatttctact attcccactc ccttctaatt tctttttgca 7800 ccccccttct ttactgactg cacctctatt ttgattactt tttgcacccc ccctgattgc 7860 taacttcaga ctatctttct tgttttttgt ttttttggtt ttttggtcag atggcctcct 7920 gtaaacaccg agctgtgccc acacccgggg aagcgtccaa ctgggactct tcacgtttca 7980 ctttcgagat tgcttggcac agataccagg atagcattca gctccggaac atccttccag 8040 agaggaatgt agagcttgga ccagggatgt ttgatgagtt cctgcaggaa ctccagaggc 8100 tcagatggga ccaggttctg acccgacttc cagagaagtg gattgatgtt gctctggtga 8160 aggagtttta ctccaaccta tatgatccag aggaccacag tccgaagttt tggagtgttc 8220 gaggacaggt tgtgagattt gatgctgaga cgattaatga tttcctcgac accccggtca 8280 tcttggcaga gggagaggat tatccagcct actctcagta cctcagcact cctccagacc 8340 atgatgccat cctttccgct ctgtgtactc cagggggacg atttgttctg aatgttgata 8400 gtgccccctg gaagctgctg cggaaggatc tgatgacgct cgcgcagaca tggagtgtgc 8460 tctcttattt taaccttgca ctgacttttc acacttctga tattaatgtt gacagggccc 8520 gactcaatta tggcttggtg atgaagatgg acctggacgt gggcagcctc atttctcttt 8580 agatcagtca gatcgcccag tccatcactt ccaggcttgg gttcccagcg ttgatcacaa 8640 cactgtgtga gattcagggg gttgtctctg ataccctgat ttttgagtca ctcagtcctg 8700 tgatcaacct tgcctacatt aagaagaact gctggaaccc tgccgatcca tctatcacat 8760 ttcaggggac ccgccgcacg cgcaccagag cttcggcgtc ggcatctgag gctcctcttc 8820 catcccagca tccttctcag cctttttccc agtgaccacg gcctccactt ctatccacct 8880 cagcacctcc atacatgcat ggacagatgc tcaggtcctt gtaccagggt cagcagatca 8940 tcattcagaa cctgtatcga ttgtccctac atttgcagat ggatctgcca ctcatgactc 9000 cggaggccta tcgtcagcag gtcgcctagc taggagacca gccctccact gacagggggg 9060 aagagccttc tggagccgct gctactgagg atcctgccgt tgatgaagac ctcatagctg 9120 acttggctgg cgctgattgg agcccatggg cagacttggg cagaggcagc tgatcttatg 9180 ctttaatgtt ttcttttata ttatgtttgt gttctctttt atgttttatg ttatgttttt 9240 atgtagtctg tttggtaatt aaaaagaggt agtagtaaaa atattagtat ttcagtatgt 9300 gttttctgag taataagtgc atgataactc aagcaatcat aattctttag cttgttcaga 9360 aaggttcaac acttgagatg ccactgatcc ttggagaaac actggttctg gaagcaaaag 9420 tcaggtcaag aaatggaaca tgaatagcac agagtggaaa ggttagcttg atggaacaag 9480 gtcataactg gtacgccgaa tacttgttta agtccctgtg agcatggttg tcaaactcta 9540 gagtcaactc atagactctc atgagtttaa gagtttactt cagtcccgcg agttgactcg 9600 gaagcaaact cgcttttgag caaactcgtg gactcggagt gaactcatgt aaactcgtaa 9660 gagtctacga gttgactcta gagtttgaca accatgcata agtgttcaaa attaaagcat 9720 ttaaataatt aaaaaaagca caaatgtctt caaagaagca tgttcaatcc tctaatagga 9780 tcatcttcat gaatatcatc actttcatca tcatctccat ctccatcatc atcatcaagg 9840 tcttcctcag attgtgcatc atcattaggt tccacaaaga ttaaattatc tagatcaaaa 9900 gcttaaaata gatatcaaat atgctatatt agaaatagtt aaaacttaaa ataatacaca 9960 agcaaatttt aaatatgaga aagttcagaa attatacctt ttcttggtgt tattaaagtt 10020 tcattttatc ttctcttttg cattttccat ctcctcacat atgaaaagca taattctatt 10080 gaatttcagt aacaagtttg atccaactcc aacattgtaa ggtcagttgt tgtgttttgt 10140 aatagactaa tatgaagtat gaagtatgaa ctatgaactt attgtcatct gtttgcaaat 10200 tggtgcattt tgaatatatt tacttattat ccattttttt ttttttacga agtagactct 10260 cacgagtctg cgtagactct cgatatcgat aaccttgccg atgagagtgt gaacttaatt 10320 gtgagagaaa atgcctattt ttaagttcct ggttttgcat cattcttaga cggttagaat 10380 agttacttaa ggtggatatg atcaaggcca tgtttgtttg tttacctact tagccaaaaa 10440 gccaacctaa catagtttta ccccttgcac ccatgattga gccaactgat tattttgaat 10500 taaccttgag ccaattaaac aaaatcctga ccttttagga ttttaagaga gtaaaaatgg 10560 gttataaagg tcttaatttg ggggattttg ggaaataggt agccaagaca ataagtacag 10620 cacacaaagt aggacacctt ttacaaacag taggcccaat ttcgaaaaaa aaatgaaaag 10680 aatttaataa agggcagaaa caaaagagca agagaggtgt caaaagaaaa gtgttgtggg 10740 gaaataaaag ggctaagtaa aaaggcctag gcagaattgg aaatttttgt tctcttttaa 10800 tcctaacttt gaatttccaa gaaaaaccat gattttttgt aagccaggcc ccgatacaag 10860 ccaataaagt ccttagtgat ccaccaaagg taactagaga taactgtaac tgagatgaaa 10920 tgcaaaattt tgaagtgtta cttgcaggtt gttatcaaat tgcaaacact aaactaggca 10980 cttgtgagca gagggaaaca ccagccttgt gaggaaagta aggcaagcca aatttgattg 11040 agttccagat gactaactga ttcaattctt ctgttgtaat gctttcattt taagatgttg 11100 acagatgcag aaaggaccag tgaaagaagg aggaactgag ccattgatag tgttggaata 11160 tttaagaact tgcttgagaa tttacttgtt tttggttttc ttggggacaa gcaaagtttc 11220 atttggggaa ttttgataac tgctaaataa ttgtgaatta atagtaaaga attattcaaa 11280 ttttggcctg aaattaatta tttagcagtt atttgtgatt aaaagttaga aaattaatta 11340 aattgaattt ttggttgcag ataagaaaat tggagttaca ttaagcaaaa aaggcaacaa 11400 aaaatgaagg aaaagaagaa gtctgaagca ggcccagccc aacacgcacg ctaagcgcgt 11460 gtcacgcgct aagcgtgcaa ggcagtacag gcgctaagcg aggcgttaag ctcgaagatg 11520 cagaatccgt tacgcgcgct aagcaagggc cacgcgctaa gcgtgcgatc caacagaaac 11580 acacgctaag cctgcatctc gcgctaagcg cgcgatctga acgcgctaag cgcgaggtgt 11640 cgcgctaagc gcgcttacga aggcccaaaa cccactttag cagctataaa tagagagtca 11700 gtccaaggga aacaacacat ctcgcctcag agcacttccc tcagcattct aagcctaagc 11760 tctccctttt ctctttgttt ttattatcct cattctttct ttcaccccca gttgtaaagc 11820 cctcaatggc catgagtggc taatctagta gctagggcct ggcaggccta aaaagccaac 11880 gatatatggt gtacttcaag agttatcaat gcaaagaaga ttcattccag gtttttttgt 11940 tctaattatt ttctttttat cttgcattca tttcttgaat ttcttttggg ttttatttgc 12000 tcgggagagg gtatttccta ataagggttt aaggattaat gcatgcatca gttttagggg 12060 ttatacgctt gggaaagggt aacacctaat agaacatctt aagaaaagaa tcatcgggtt 12120 agcattgcta ggcatagaat gataactcaa tgcccacgca tttagcaaca tctagaattt 12180 taccttaatg cattttaatt attgagtctt cgcaaaggca tttgggagat aggtagttaa 12240 aataggcttg tcatcgtgag gcatcagggg caagtaaaat taatagatgt gggtagaact 12300 gttacaaatg cattggtaat gaatatcata tttacatgca tcgtaggcca attgggtttg 12360 tccggtcttg gcatttatat taattgtctt tctaaaacta tttgatctag taatagcaat 12420 ctattcttgc acttactcct gtttttacta ttttactctt acaaattgaa aagtattcga 12480 taaagtgcaa taaaatccct gtggaaacga tactcggact tccgaggttt actacttaga 12540 gcgatttggt acacttgcca aagtctcaac a 12571 21 4609 DNA Glycine max 21 gatctcccat atcctatggt acccaccaag aagaacaagg aacattactt ctgacgtttc 60 ttggaaatat tcaaaggact ggaaatcacc atgccattcg gggaagcctt acagcagatg 120 cccctctact ccaaatttat gaaggacatc ctcaccaaga aggggaagta tattgacaat 180 gagaatattg tggtaggggg caactgtagt gcaataatac agaggaagct acccaagaag 240 tttaaggacc ccggaagtgt taccatcccg tgcaccatag gaaaggaaga ggtaaacaag 300 gccctcattg atctaggagc aagtatcaat ctaatgccct tgtcaatgtg cagaagaatc 360 aggaatttga agatagatcc caccaagatg acacttcaac tggcagaccg ctcgatcaca 420 agaccataca gggtggtaga agatgtcctg gtcaaggtac accacttcac ttttccggtg 480 gactttgtta tcatggatat cgaagaagac acagagattc cccttatctt aggcagaccc 540 ttcatgctga ttgccaactg tgtggtggat atggggaatg ggaacttgga ggtgagtatt 600 gacaatcaga agatcacctt tgaccttttc aaggcaataa agtacccata ggagggttgg 660 aagtgcttta gaatggagga gattgataag gaagatgtca gtattctcga gacaccacag 720 tcttcgctgg ggaaagcaat ggtaaatgct ttagactgtc taaccagtga agaggaagaa 780 gatctaaagg cttgcttgga agacttggat tgacaagaca gtattcctaa gggagaagcc 840 agatttgaga ctctagaaaa ggaagttccg tccgagaaga agaagataga gttgaagata 900 ttgcccgatc atctgaagta tgtgttcttg gaggaagata aacctgtagt gatcagtaac 960 gtactcacaa cagaggagga aaacaggtta gtagatgtcc tcaagaaaca cagggaatca 1020 attggatggc acacatcgga tctcaaggga attagccctg cttactgcat gcacaggata 1080 atgatggaag aggactacaa gccagtctga caaccccaga ggcggctgaa tccaacaatg 1140 aaggaagagg taagaaaaga ggtactcaag ctcttggagg ttgggctcat ataccccatc 1200 tctgacaacg cttgggtaag cccagtacag gtggttccca agaaaggtgg aatgacagtg 1260 gtacaaaatg agaggaatga cttgatacca acacgaacag tcactggctg gcgaatgtgt 1320 attgactatc acaagctgaa tgaagctaca cggaaggacc atttcccctt acctttcatg 1380 gatcagatgc tggagagact tgcagggcag gcatactact gtttcttgga tggatactcg 1440 ggatacaacc agatcgcggt agaccccata gatcaggaga agacggtctt tacatgcccc 1500 tttggcgtct ttgcttacag aaggatgtca ttcgggttat gtaatgtacc agccacattt 1560 cagaggtgca tgctgaccat tttttcagac atggtggaga aaagcatcga ggtatttatg 1620 gacgacttct cggtttttgg accctcattt gacagctgtt tgaggaacct agaaatggta 1680 cttcagaggt gcgtagagac taacttggta ctgaattggg aaaagtgtca ttttatggtt 1740 cgagagggca tagtcctagg ccacaagatc tcagctagag ggattgaggt tgatcgggcg 1800 aagatagacg tcatcgagaa gctgccacca ccactgaatg ttaaaggggt tagaagtttc 1860 ttagggcatg caggtttcta taggaggttt atcaaggatt tctcgaagat tgccaggccc 1920 ttaagcaatc tgctgaataa agacatgatt tttaagtttg atgaagaatg ttcagcagca 1980 tttcagacac tgaaaaataa gctcaccact gcaccggtaa tgattgcacc cgactggaat 2040 aaagattttg aactaatgtg tgatgctagt gattatgcag taggagcagt tttgggacag 2100 aggcacgaca aggtatttca caccatctat tatgctagca aggtcctgaa tgaagcacag 2160 ttgaattatg caaccacaga aaaggagatg ctagccattg tctttgcctt ggagaagttt 2220 aggtcatact agatagggtc gagggtcacc attttcacag atcatgctgc catcaagcac 2280 ctgctcgcca aaacagactc aaagctgagg ttgattagat gggtcatgct attacaagag 2340 tttgacatca ttattaagga caagaaagga tccgagaatg tggtagctga tcatctatct 2400 cgattaaaga atgaagaagt caccaaggaa gaaccagagg taaaaggtga atttcctgat 2460 gagtttcttt tgcaggttac cgctagacct tggtttgcag acatggctaa ctacaaagcc 2520 atgggaatca tcccagagga gtttaattgg agtcagagga agaaattttt gcacgatgca 2580 cgcttatatg tgtgggatga tcctcatttg ttcaaggcgg gagcaaataa tttattaagg 2640 agatgcgtca caaaggagga agcacgaagc attctttggc actgccacag ttcaccctat 2700 ggcatacatc acagcgagga tagaacaaca gcaaaagtgc tacaatcaag ttttttctag 2760 ccctttattt ttaaagatgc tcacgagttt gtgcattgtt gtgataaatg tcagagaaca 2820 agggggatat ctcgaagaaa tgagatgcct ttgcagaata tcatggaggt agagatcttt 2880 gatagttggg gcatagactt catggggcct cttccttcat catacaggaa tgtctacatc 2940 ttggtagctg tggattacgt ctccaaatgg gtggaagcca tagccacgct gaaggacgat 3000 gccagggtag tgatcaaatt tctgaagaag aacatttttt cccatttcgg agtcccacga 3060 gccttgatta gtgatggggg aacgcacttc tgcaacaatc agttgaagaa agtcctggag 3120 cactataatg tccgacacaa ggtggccaca ccttatcaca ctcagacgaa tggccaagca 3180 gaaatttcta acagggagct caagcgaatc ctggaaaaga cagttgcatc atcaagaaag 3240 gattgggcct tgaagctcga tgatactctc tgggcctata ggacagcgtt caagactccc 3300 atcggcttat caccatttca gctagtatat gggaaggcat gtcatttacc agtagagctg 3360 gagcacaagg catattgggc tctcaagttg ctcaactttg acaacaacgc atgcggggaa 3420 aagaggaagc tacaactgct ggaattagaa gagatgagac tgaatgccta cgagtcatcc 3480 aaaatttaca agcaaaagac aaaggcatat catgacaaga agctacaaag gaaagaattc 3540 cagccagggc agcaggtatt actcgttaac tcaaggctaa ggctattccc aagtaagctg 3600 aagtccaatt ggtcagggcc attcataatc aaagaagtca gacctcacag agcagtagaa 3660 ttggtggacc ctagagaaga gaactttgat aagaaatgga tcatcaatgg acagcgcttg 3720 aagccttata acggaggaca actagagcga ttgacgacca tcatctactt aaatgaccct 3780 tgagaaggcc tactgtcgag ctaaagacaa taaactaagc gctggttggg aggcaaccca 3840 acatattttg taaaaatgta gttatcttca ttctatgtaa aaaaaaagcc caacaggtgc 3900 aaataggaaa cacgaggtgc aaaaagcaaa ggcccaacat gtgaagacaa caataggagg 3960 ggtgccaata gcaaaactga agtgggctac acgaagctac gtgcttagct cgcgtccgcg 4020 cgctaagcgc ccagattgca caaaaatagg tgagacttgg aatctggact attgctgtaa 4080 tatcttgcag gtaccattac gctaagccct acacagaggc ttagcgagaa caggcagcat 4140 ggaaaaaggg aaggaggagc gcgctaagcc acaacaagta atagaagaaa acgaagcacg 4200 cgcttagcgg gcactgccgc gctaagcgca ctcttcaaca tcagtgaacg cgctaagcgc 4260 gtgccagaag cgctaagcgc gtgtcaccgt caccagcagg aaggcgctaa gcgcgaggtt 4320 gggccttagg gcccatcagc cttcgcgcct tactttttgc acaccccttc tttactaact 4380 gcacccctat tttgatttct ttttgcaccc cctctgttta ctaactgcag tttgtttctg 4440 ctgtttcttg tttttgtttc agatggcctc ctgcaaacgc cgagccgtgc ccacacccag 4500 ggaagcgtct aattgggact cttcccgttt cacttcagag attgcatggc acagatatca 4560 ggacaacatt cagctctgga acatcctttc ggagaggaat gtcgagctc 4609 22 9139 DNA Glycine max 22 acctggttgt ttgtatgctt gtcttaatgc ggataggttg tcaagtagct ttagtgctaa 60 cactgagaag aatccgaagg aagaatgtaa agttttaatg acaaagagca gaatggaaat 120 tcaagttgat gaagttagag ctgaagagaa ggtggaggga tataaacaac agtcgatagc 180 tgagcctgca ctggaactag tttccgatct tattgaactt gaggaagttt tggaagagga 240 agatgaccaa caggagagag agacaccaat aaaagatagt caagaaggaa taaagatgaa 300 ggaagagcat gaaaaagaaa aacaaaaaga aaaagaagaa atagaaaaag aaaataataa 360 aaaaaatgaa aaataaaaaa agatggttga tgaggagaaa aaaaagagca agagtgaggt 420 ttcaagagaa aaaaagagag agattacttc agctgaaggc aaggaagtac catatctatt 480 ggtaccttcc aagaaggata aagagcaaca cttagccaga tttcttgaca tcttcaagaa 540 actggaaatt actttgcctt ttggagaagc tctccaacag atgccactct atgccaaatt 600 tttaaaagac atgctgacaa agaagaacta gtatatccac agtgacacaa tagttgtgga 660 aggaaattgt agtgctgtca ttcaacacat ccttccccca aatcataagg atcccggaag 720 tgtcactata ttatgttcca ttagcgaggt tgttgtgggt aaagctctca tagacttggg 780 agctagtatc aatttaatgc ctctctcaat gtgtcgacga cttggagaga tagagataat 840 gcccacacgc atgacccttc agttggttga tcactccatc acaagaccat atggagtgat 900 tgaggatatg ttgattcagg tcaagcaact tgtattccct gtagatttcg tggttatgga 960 tatagaggag gatcctgaca ttcccataat cttgggacgt cctttcatgt ccgcgaccaa 1020 ctatatagta gatataggga aaggcaagtt agaattgggt gtggaggatc agaaagtctc 1080 attcgactta tttgaagcaa ataagcatcc aaatgataag aaagcttgct ttgatctaga 1140 caaggtagaa caataaatag aattagctac tatagccatg gtactgaact ctcctttgga 1200 aaaagcattg attaatcatg tagaatgtct tactaaagag gaggaacatg aagtgcaaac 1260 ttgtattaaa gagttggatg gtgcaggaga aaattctgag ggacaggatg catttcaaga 1320 attgaagaat ggtgggcaaa tagaaaaacc aaaagtagaa ttgaagacct tgcctgcaca 1380 tttgaagtat gtatttctcg aagacaatga ctccaaacca gtgattatta gcagctcgtt 1440 gaagaaaata gaagatcaac tggtgaagat tttgaagaga cacaaagctg caattggatg 1500 gcacatatct gacttgcaag gaattagtcc atcttattgc atgcacaaaa tcaatatgga 1560 agctgattac aaaccagtga gagagcctca aagaagactg aacccaatca tgaaagaaga 1620 gatgcataag gaggtgctta aattgtagga agcaggcctt atttacccct cctcggatag 1680 tgcatgggtt agccttgtgc aggttgtccc caagaaagga ggtatgacag tcattaaaaa 1740 tgataaagat gagttaatat ccataaggac tgtcaccggg tggagaatgt gcattgacta 1800 tcggaagctg aatgatgcca ctcggaagga ccattatcca cttcctttca tggaccaaat 1860 gcttgaaaga cttgtagggt aatcctatta ttgttttctc gatgagtact ctggctataa 1920 ttagattgtt gttgatccta aagatcaaga gaagactgct ttcacctacc cttttggtgt 1980 attcgcatat cggcacatgc cttttggtct gtgcaatgcc ccagctacat ttcagaggtg 2040 tattatggca attttttctg atatggtgga aaaatgcatc gaagttttca tggatgattt 2100 ctctattttt gggccatcct ttaaggggtg cctattaaat cttgaaagag tattacagag 2160 atgtgaagag tccaatctag ttctcaattg ggagaaattc catttcatgg ttcaagaagg 2220 aatagtgctg gggcataaaa tttcagtaag gggaatagag gtggacaagg caaagattga 2280 tgtaattgag aaacttcctc ctccaatgaa tgccaaagaa gtgagaagtt tcttatgaca 2340 tgcaggattc tacagatgat tcataaaaga tttctcaaaa gtcgcccagc cacttagcaa 2400 tctgttgaat aaagatgttg cttttgtgtt caatcaagag tgcatggaag catttaatga 2460 tctgaaaacc agattagtgt ctgctccagt aagtatagca ccagattggg gacaagaatt 2520 tgagttgatg tgtgatgcaa gtgactatgt cgtaggtgta gtgcttcgac aacggaaggg 2580 aaaacttttt catgctatat actacgccaa caaggttcta aatgatgcac aggtgaacta 2640 tgctaccata gaaaaagaaa tgctggcaat tgtctatgca cttgaaaagt ttagatctta 2700 tttggtaggt tcaagagtta tcatctacat cgatcacgca gctattaaat atttgctcaa 2760 caaggctgat tccaaaccta gattgataag atggatcttg ttgttgcaag aatttgattt 2820 ggtgattcgg gataaaaagg gatcggaaaa tgttgtagct gaccatttgt ctagattggt 2880 gaatgaggaa gtcacattga aagaagcaga agtgagagat gaattccctg atgaatcatt 2940 attcttagtg agtgagagac cttggtttgc cgatatggcc aacttcaaag ctacaagaat 3000 catcccaaag gacttaactt ggtagcagag gaagaaattc ctacatgatg ctcgattcta 3060 tatctgggtt gatcctcatt tgttcaagat aggagctgac aatctcctat gaagatgtgt 3120 gacacaagaa gaggccaaga acatattatg aaattgccac aattctccat gtggcagcca 3180 ttatggtgga gataagacga tgaccaaggt tttgcaatct ggattctttt ggcccatgct 3240 tttcaaagat gctcatcagc atgtgcaaca ctgtgatcaa tgtaagagga tgaggggtat 3300 atcaagaaga aatgaaatgc ctctacagaa tattatggag gttgaggtat tcaattgcta 3360 ggggattgat tttgtaggtc ccttcccttc gtcttttggc aatgaatata tactagtggc 3420 gattgactat gtctctaaat tggttgaagc agtggctacc ccgcataatg atgctaagac 3480 tgtggtaaag tttctaaaga aaaacatttt ctcaagattt ggggtgccta gaattctgat 3540 taacgatgga ggcacacact tctgcaataa tcatctatag aaggtgttga agcaatataa 3600 tgtgacacaa agtagcatca ccttatcacc cccagaccaa tgggcaagca gaagtatcaa 3660 acagggaatt gaaaaagatt ttggagaaga ctatagcttc tactagaaaa gactagtcta 3720 tcaaattaga tgatgcttta tgggcataca gaacaacatt caagactccg ataggattat 3780 ctccatttca gatggtgtac ggcaaggctt gtcacttacc agtggagatg gaatataaag 3840 catactaggc cttgaagttt ttgaactttg atgaagccgc atccagagaa caaaggaggc 3900 tgcaactttt ggagttggga gatatgagat taactactta tgaatcttca aggctataca 3960 aagaaagggt caaaaagtat catgacaaga agctgctcaa gaaggacttt cagccaggac 4020 gacaagagtt gcttttcaac tcaagactta aattgttccc tggaaagctt acatcgaaat 4080 ggtctggacc atttaccatc aagaaagtcc gcccatatag agcagtggag ctttgtgatc 4140 ctcaatctaa agatcctgac aggacatggg tagtgaacgg acaaaggttg aatcaatatc 4200 atggttcatg caatcctacc cctcaagggt attggataga agactccaag aggattgggc 4260 tagagctgct aaagaaggcc ttggggttct catgaacccc agggtaaatt tctgagccca 4320 tggaccaagg ttgggtcctc tcttctttgt aaatattaga ataggttttt ccttcttctc 4380 aggctaagca ccaatatgct tctgtttttc agtcctttga ataaggctaa gcgcagctgc 4440 tgcactaagc ccttgttgtg tgtcaaggag gttgagctaa gcgtgcccta ctgcgctaag 4500 ctcaactatc tcactatttt tgtgttttta tggtcaggct aagcgcgccc tatgtgctaa 4560 gcctaagggt cattctggtg agcgtgagct aagcgcgcca tgctgcacta agcttagacc 4620 cttttttgtt ttgaaaattt tagacttagg ctaagcccaa catgctacgc taagcctatc 4680 tacagaaaaa tattttgtgt ctttaggcta agctcgagtc tactgcgctt agctcatgag 4740 taatatttta taaggcgcgc taagcccagc ctgctgcgct aagtgcccag ttcagttttc 4800 agctttaatt ttttgttttt gatagaaata atcttattta accttgtggt ttgattttat 4860 tctttcagat agcatcaaag aagagaaagg cacctgccac accttcccag gtctgatatg 4920 gccgatcgag gttcacttct cttgtggcct aggaaaggta cactgatatt gtggtaccca 4980 ggaagatact ccctgagtgg aatgtggtaa tctaccacac tgagtttgat gagtttaagg 5040 aagaactaga gagaagaaaa tgggatgagg aattgaccag ttttgatgaa ggcaacattg 5100 atgttgccat tctgaaagag ttttatgata acctctatga ttccgacgat aaatcaccta 5160 agcaggtgag ggtgagaggc catttggtga agtttgatgc agacactctg aacactttct 5220 tgaagacccc tgtgataatt gaagaggggg aaaagctgcc tgcctactct agatttgcac 5280 tcttgagtcc tgatcctcaa gagttggctg ctaagctctg catcccaggg agggaatttg 5340 agcttaatgt tgacgacttg ccactaaaga tcctcaggaa gaaaatgacc acactcgctc 5400 agactaggag tgttctttct tactccaact tggtccctac ctcccacact tctcacatca 5460 cactggatcg ggccaagttg atttatggca ttatcatgaa gatggacatg aatttgggct 5520 acctcatctc ccaccagatt tctatcattg cccagcatga ctcctctagg cttggattta 5580 caaccttaat catagctttg tgtaaagcta aaggagtcac attagattcc aaatctttgg 5640 agagtcttag ccctgccatt aacatggcat atataaagaa gaactgttgg aatctagatg 5700 atccaacagt gacattcaga gagccaagga aggccagggg taaaagaatc gaggctcccc 5760 ctacttcagc agcaccaggt gcttctgctc cttcttcatc ttctttacca gatccttcag 5820 caccatccac ttcgactcca catcttccat ggttactagc ttcagctccc actcccttac 5880 cagcttcaat tcagctcctt ctacaggacc ctcctcattc acctctaaga cattatttgc 5940 tatgctgcaa agcctgcaca aaggccagat catcatcata cagaggttgt agagctctgg 6000 ccagaaacca accatgagta tagaggagtt ccttgcacaa gtggcttgcc caggagtcga 6060 gccttctcct tctggagggg gtgaggcctt tgcagcccaa gagccttgcc agcagagaag 6120 cctgtgccag aagcagagga tgagcttgtt cttcctgagc catttgttta tgagattgat 6180 ccagtcgctc aggaggaagc agcagctcag gagcttcctg cacctatttc tgaggatacc 6240 ctgccatctg caccagcatt ggagtaagag cagcctagtt cacaggatcc accagctgct 6300 ccaatgctgg atctgaacga gcatgcagaa gatcagcagt aggatgatca tgagttttaa 6360 attctacata gtttttaaaa ttttgcaaat tatgaatagt ttcttttatc aattatttag 6420 ttcatgtcaa ttatttgttt atgctttatt agtctttaaa ttttagtctt ttaaattttt 6480 gttgtttgag tgttgatagc ttgtacaaaa gcatgtttga acagtgaact tattgattat 6540 gatattcagt ggtgtgattt cttatgaatg aagtgtttgt gaatgacttg aatgagaaaa 6600 tgtatgaatt gagtggactg gaatgattag atgtttgttt tgatcaagct tgtagtcatt 6660 agaagaaaaa gaacatgtga ttagaagtat gactgaaaat gttagtcagt ttgtcaaatt 6720 gattgtgaag gaatgcattg accgtatccc agtgagagtg tgatccttaa attttgagag 6780 aaatgacttt aatttagcac taatttttgc acgaatcttt gaagtatgga ttgaatgcat 6840 gaattgagga taatgaaggc catgttttga ttgtgatagc tatttagcca aaaagctgac 6900 cttgtgcttg aatgatttat cccttgcacc cagtttgagc tgaatgaatt attgattgat 6960 tgaaccttga gcctatatag tgttttctcc tgcttccttg tcttaggtta taggagagca 7020 taatccacag aaaagcttgg ttcaaggcaa atttgttcca aatttggggg agacactggg 7080 taaagaaata aaatggtcaa aacagagcaa catatacaca ttgttttctg tatgtaaaaa 7140 aaactgtaag tataaataaa aatgtataaa agtgtgtgtg ctgcaaatca aatcaatgaa 7200 agctaagtgc ttaataaaag gcaagtatgg ggtaggaatg aataaaaaaa aaagtaaagg 7260 tttatctatg gatgaatgct ctcgtagaat ctaagctttt gaatcctaga aaaaccatga 7320 tttgttggca gcctaacctc attacaagcc tagaaagtcc tttggattca ttttgtgtgt 7380 ttatttctgt atggtatgag atgaaatgca aaagttagga cttgtgttag ttgttcatga 7440 tggaatgagc ctaaacactt aagcttgagt gaaacaatga ctgtgaggct ttggttgatg 7500 attttttcct tgatatctgt cattctcact agcttatttt agttgtgact ctaatgcata 7560 tgttcctatc tttgaaaaac tgcatgtttg tgaaaagaaa ttggttgaag cattccatga 7620 tattcatttc atatgattga atttctctgt gaggagaaca ccatttggat tgaccactgt 7680 attttgtcac ttgaggacaa gtgaactgtt ctttctttgc ttgaggacaa gcaaaacttt 7740 aaatttgggg gagtatgtta gtcatcttat acgactaact tttgtataga aaaaattttc 7800 caaaacttgt atagtttctc caatttatag ttattttgta gggatttgta aataaatctt 7860 gttttattgt tatagttgtc tctagaatat tttccatttg atttaatgat gaaatctgtt 7920 caatttcagg ttaaaagagg ctaagtcttg aagtgctaaa agtgggattt acgctcagct 7980 caccatttgg cctcaacgcg catccaccgc taagcacagc ttcagcgcac ttagtgtgac 8040 agaagaatct ggcagagcat aaatatcaag gccgcttgct aagcaagatg gttgtcttta 8100 gccagactca gcgcatgact ggcgctaagc tcaaatccac taactcgcgc taagcacagg 8160 ggtggcacta agtgcaacgt cgcggattta aagcctattt aaagcctgtc ttgtgcagaa 8220 ttaggtaata tacacacata gaattttagc aagcaataca aaattccaaa gcaaggacac 8280 cacagtgcta atttcgatat agaagctctg gaggcagcaa gaggagaagc tttgcagaga 8340 agcctaggat tcttcaatta gagagagatt agtgagctgt agagtgattg tgaggtgttg 8400 agaagaggag gagggatccc ccttcttgtg taaggaacaa ttatttggta ctctcaaact 8460 catttgtgtt agggtttttc tgtaatggct agctaaacac ccttgttggg gatttctaag 8520 gaacaactga tgtaattact ttaatatcta attaattatg ttttatgtgt tcaatgcttc 8580 tttcaatgct taattactgc atgctcttgg tctgatcacc catttgtgtg tattgttagg 8640 tgactttagc attgggaaat gtaccgttgc cttagaactt gatagaagca ggactaaata 8700 actacattac cagggatgga ttatggggtt ttggttttct aaatatgttg tgatgataat 8760 gctatttaag ttaagcctag tcatacaaga gggatctgcg gacgaagctt aggttaaatt 8820 agtataaact tacaagggat cgagatttag tactttaggc tacaacatag aacacaagaa 8880 catgattaat tagagaaata tcctcatatg catcaacttg tttgttagaa agacccaacg 8940 ctttttacct attgttgtca acttttactt acttgcattt tttttttacc atagaagtag 9000 tttatttctg ttttaaccat caattatcaa tgttgttcca acaatgcctt acttctgaat 9060 aaaactctgt ctaataagca agttccctaa attcgatact tggatcactc tgttttaatt 9120 ttaaatactt gacaactca 9139 23 10482 DNA Glycine max 23 tgttagtcgt cttatatgac taacttttgt atagaaaaac ctttttcaaa acatgtatag 60 tttccccaat ttataattct tttgtaggaa tttgtaaata aatcttgata tgttttgata 120 cctgccatta gagtatcttt agttggagtt aatgagaaaa tttgtacaat ttcaggtcaa 180 aagaggctaa aatcttgaag tgctaaaagg agcagtcgtg ctaaatagag cctgtgggct 240 cagtgcacat ccaccgctaa gtgcagcttc agcatgctta gcgtgacaag ggaacctgaa 300 agagcacaag aatcaaggtc gcgcgctaag cgagacgttt gtcttttgcc aggctcagcg 360 cacgactggc gccaagccca aatccactta ctcgcgctaa gcgcgatgtc gcgatttcag 420 agcctattta agcctgaatt gtcagaatta gggtatgatt ttaagagacc agagctgtat 480 atttttgcac aaacttcgag aatagtgctc tggaggcagc agagaggcag cagctaagca 540 gggaagctag ggttcatcac tttgagagat tagagagtgt tttagtgatt gtgaggtgcc 600 aagaagacga ggagggatcc cccttcctgt gtaagcaaca attgctctgt actttctgtc 660 tcatttgtat tagggttcct tgtatggctt ggtaaaaacc ctagttgggg atttctaatg 720 aacagttgat gtaattactt ttcatatcta attaattgtg ttttgtgtgt tcagtgcttc 780 tttcaatact taattactgc atgctcttgg cctgatcacc ctcttgtgtg tactattagg 840 tgactttagc attgggaaat gtagtgctgc catagaacat gatagaagca aggctaaata 900 actgcattac ctaggatgga ttgtggggtt ttagttttct tattatgctg tgatgataat 960 gttgtttaag ttaagcctag tccaacaaga gggatctgag gatgaagctt gggttaaatt 1020 agtctaaact tatgagggat cgaggtttag tactttaggc ttcagcatag aacacaagaa 1080 catgattaat tagagaaata tcttcatatg cattaactcg tttgttagaa agacccaaca 1140 ctttatacct attgctgtca actttttaat tacttgcatt tactgctttt taacatagca 1200 tctagtttac ttttgtttat attctcaatt atcaatgttt gttcacacaa tgccatattt 1260 ctaaataaaa ctttgtctaa taaacaagtt ccctgagttt gatactcgga ttattccgtt 1320 ttaattttaa atgcttgata acctggtgcg ttttccgata tttcatttcc cttgaatata 1380 ctgcttgtaa atttgataga aaggaactgt gttgaagggt aaacaaaaat ttgacacaaa 1440 gcatttatgg cgccgttgtc ggggaactgg attcattaga agagttcagt tcagttttaa 1500 ggcattgctt tattttgttt tctttaattc attgattctt tttgctaaca ttttagttac 1560 tgcacatttt attgttcttt ggaattggat aatttttgtt ttgtttcttt tgtatgcaaa 1620 ggagatctgt tgtaggtgat ttaattccca tagatttgga gattaatgct acttgcagga 1680 gacaaaatgc agagagaatt agaaattttt tgcaggactt agaagtagca gcaactctag 1740 gagagtgacc ctagaagatt actcaagtta aggccacagt ccaagcagct attagatgct 1800 tctgctgggg gaaaaataaa gttaaagacc cccgaagaag ccatggaact cattgaaaat 1860 atgactgcaa gtgacattac tattttgaga gatagagccc acattccaac aaaaagaagc 1920 ctactagagc tttcatcaca agatgcattg ttggcacaaa acaagttgat gtccaagcaa 1980 ttggaagcat tgaccaaaac actaagtaag tttccagctc aattacattc tgcacaatct 2040 ttaccatcta ctattttgca ggtcacagtg tgtgccatct gtggtggagc tcacgattct 2100 ggttgttgta tccccaatga agaaccaaca actcatgaag tcaattacat gggtaaccaa 2160 cctagaaata attttaatgc aggtggattt cccgaattcc agcatggaca gtaatacaac 2220 caacaacagg gacaatggag gaccaccctg ggaattaatt caatagagac cagggtggac 2280 cgtccacaag gccgtaacaa caagggccta gtctctatga gcgtacaacg aagttggaag 2340 agactctagc tcaatttatg caggtttcta tgtctaacca aaagagcacg gagtttgcca 2400 taaagaattt ggaagtccaa gtgggacagc ttgcaaaaca gttggtggat aggccgtcaa 2460 agagctttag tgctaacact gagaaaaatt cgaaggggga atgtaaagct gtcatgacaa 2520 gaagcagaat ggcaacccat gttgatgaag gaaaagctta gaagaaggtg gaggagcata 2580 aacaacagtt ggcagctgag ccggcacttg aacccatttc tgattttgtt gaacttgagg 2640 aagttatgga agatgaagat gaccaaaagg aaaagagaaa gaagaagtag aaaaagaaaa 2700 atattagaaa aatgaaaaag aaaatgagaa ggttgaggaa agaaagagga gcaagagtga 2760 ggtttcaaga gagaaaaaga gagagattac ttcagctgaa ggcaaggatg taccatatcc 2820 attggtacct tccaagaagg ataaagagcg acacttagcc agatttcttg acatcttcaa 2880 gaagtcggag atcacattgc cttttggaga aactctccaa cagatgccac tctatgccaa 2940 atttttaaaa gacatgctga caaagaaaaa ctggtatatc cacagtgaca cgatagctgt 3000 ggaaggaaat tgtagtgctg tcactcaacg catccttcca ccaaagcata aggatccagg 3060 aagtgtcaca ataccatgtt ctattggtga agttgcagta ggcaaggctc tcattgactt 3120 gggagccagt atcaatttaa tgactctctc catgtgccag caacttggag agttagagat 3180 aatgcccact cgcatgaccc tacagttggc agatcgctcc attgctagac catatggagt 3240 gatcgaggat gtgttgattc aggtcaagca gcttgtattc cctgcaattt tgtggttatg 3300 gatatagagg aggatcctaa cattcccata atcttgggac gtcctttcat gtccacgacc 3360 agctgtgtag tagatatggg gaaaggcaaa ttagaactgg ttgtggagga tcagaaagtc 3420 tcattcgact tatttgaagc aatgaagcat ccaaatgatc aaaaagcttg ctttgatctg 3480 gataaggtag aataggagat agaattagct gctatagcca tggtactgca ctctcatttg 3540 gaaaaagcac gattaatcat gtagaatgtt tgaccaagga ggaggaacat gaagtgtaga 3600 cttgtattaa agagttggat ggtgcaggag aaaattccga gggacatact gcatttgaag 3660 aattgaagaa cagtgggaaa atagaaaaac caaaagtaga attgaagact ttgcctgcac 3720 attcgaagta tgtatcttgg aagacaatga ctccaaacca gtgattatta gcagctcttt 3780 gaagaaaaca gaagaagatc agttggtgca gattttgaag aaacataaag ctacaattgg 3840 atggcacata tctgacttga aaggaattag tccatcttat tgcatgcaca aaattattat 3900 ggaagctgat tacaaaccaa tgagacagcc tcaaagaaga ctgaacccaa tcatgaaaga 3960 ggaggtgcgc aaggaggtgc ttaagttgct agaagcaggc ctcaccccat ctcagatagt 4020 gcgtgggtta gcccggtgca ggttgttctc aagaagggag gtatgacagt cattaaaaat 4080 gataaagatg aattaatatc cacaaggact gtcaccgggt ggagaatgtg cattgattat 4140 cggaagttga ataatgccac ttggaaagac cattatccac tccctttcat ggaccatatg 4200 cttgagagac tcgcaaggca atcatattat tgttttctgg atggatattc tagttacaat 4260 tagattgcta tagatatcaa agatcaagat gtcgcaacct acccttcagt gggagggcga 4320 cgcgtgactt gcgcgtgcat gttccaagaa aggaatacgc gcggagtcgc caccaacgtt 4380 tatttgagga aaacgtcgga aaaaccggaa aagacgtgat ctacgaactt taagtgaaag 4440 gttcgggagt tgtatttacg cacggggaag gtattagcac cccacacgtc cgtcacaaga 4500 gatgacaacc tctaatcaaa tgtgcaaata tgacttcaat ttatgttatc ttcccccttt 4560 tttcacgttc ttatgttttt tttatgcctt tttatgtttt tatctttttg tggttgacaa 4620 gggcgtttcc ctttgctcct acgtattcct caattgtgat gagaaaatca aacctacgta 4680 gttcttttgt gaacaaagcg ttttggttaa gttatttttt atcctttttt gcaagatatg 4740 ttttattgaa tgaaaggtca tttaaggtgt tggaccatta gacaatcttt cgattctttt 4800 gaaaagtgag aaaacattaa ggcattggac cattaatgat ttctttattt ttgaaagagt 4860 taacaaagtt acatattgat tttaggcttt ttagaaatct acacttaacc aataaaagcg 4920 gaaaagacca tttcaaggcg ttggaccttt gaaaaatggc gtttttaggc gatgacaaaa 4980 gtttggttta tgaattgatt ttagccttag tttcactttg gttattagtc gattcgattt 5040 aagaaagaga aatcccaaag aaaaacgtcc gattgatttt ttgatttatt ttactaaaag 5100 atatttttga ttattatatt attattttac ctatttttgg ttttcaacgg gttacggcat 5160 gaccgaacag tcggatttca ttttaacaga aattaacgga tgttacaatt taaatgatcg 5220 gtggaaattt attttatttt ttgattaggc gagaaaatga cttaagtaaa tgactaaagc 5280 acgtcaaaag ggggtacgga aagtaaatga aatgaaaata aaagcatgtg aaacaaatga 5340 ggaccactaa gggtacatag aatgaattgt ttgatttcgg gaacttaccg gttgaagatc 5400 gaagaacgac gaagaacgaa cgaagaacgt cgatgaacgg ttgaaaatct tcgcaaaatc 5460 acccacggaa acgttacgga agcacctcgg cttggatttt cttcacggaa acaatttttc 5520 tcactaattt taagtgaatc tcagatacca ggagggtcga acatttttgt tcttccctcc 5580 ttcccttatt tataggaaaa ggaaggagat gcttgccacc cagctcgccc aggcgagcta 5640 ggttgcttcc tccagaagca aatcctggaa ggcccaagtg ggcctggttg ctatttgaac 5700 ccccaatttt actaaatata ccccctgcct ttttttggtg attctttttc cgtaaagtta 5760 tggaaactta cgaatttcgt aacgatactt gttttctttc cgtaatgttg tggaacctta 5820 cggattacgt aatcatccct tttttgcctt ccggaacgtt acagaacttt acggattgca 5880 cactaacact tccttttaat tttcggcatg tcacgaactt cacggattgt gctaccacgc 5940 ttttcttttg gcttccgaca tgtctcggaa cttcacaaat tgcctaacca tgggtgccaa 6000 atacctcgaa gtggtcaaac gacggtcgca tcccaacaac ggatggttct cggacgaaat 6060 tagggtatga cacaagagaa gacaactttc actttccctt tcggtgtatt tgcatatcga 6120 tgcatgcctt tcggtctatg caatgcccta gctacatttc agaggtgtat gatggcaatt 6180 ttttctgata tggtggaaaa atgcattgaa gttttcatgg acgatttctc tgtttttgga 6240 ccatctttga tggttgctta tcaaatctgg aaagagtatt ttagagatgt gaagagtcca 6300 acctggtact taattgggaa aatgtcattt catggttcaa gaaggaatag tgctggggca 6360 taaaatatca gtaaggggaa ttgaggtgga taaggtgaag attgatgtca ttgagaaact 6420 tcctcctcca atgaatgtca aacgaatgag aagtttctta ggacatgatg gattctatag 6480 gtgacttata aaagattttt caaaagtcgc caaaccactt agcaatttgt tgaacaaaga 6540 tgttgctttt gtgttcaatg gaaagtgtat tgaagcattt aatgatttga aaaccagact 6600 agtgtctgct ccagtaatta ctacaccaga ttgggggtaa gaatttgagt tgatgtgtga 6660 cgcgagcgat tatgctatag gtgcagtgct tggacaaagg aagggcaaaa tttttcatgc 6720 tatctactac gccagcaaag ttttaaatga tgcacaggtt aactatgcta ccacagaaaa 6780 agaaatgttg gcaattgttt atgcacttga aaagttcaaa tcttatttgg taggctcaaa 6840 agtcatcatc tacattgatc atgcaactat taaatatttt ctcaacaagg ccaattccaa 6900 aaccctgctt aataagatgg attttgctgc tgcaagaatt tgatttggta attcgggata 6960 aaaagggatc ggaaaatgtt gtagctaacc aatttgtcta gattggggaa taaagaagtc 7020 atgtcgaaag aagctgaaat tagagatgaa ttccctaatg agtcattatt cttggtgaat 7080 gagagacctt gatttgctga tatggccaac ttcaaagccg caggaatcat tccaaaagac 7140 ctaacttggc agtagaggaa gcaattcctg catgatgctc gattttatat ctgggatgac 7200 ccgcacttgt tcaagattgg agttgacaat cttctccgaa gatgtgtgac acaagaagaa 7260 gccaagaaca tattatggca ctgtcacaat tctccatgtg gcggccatta tggtggagat 7320 aagacgacga ccaaggtttt gcaatctgga ttcttttggc ccacactttt caaggatgct 7380 catcagaata tgctgcattg tgatcaatgt caaaggatgg ggggcatatc aaaaagaaat 7440 gaaatgcctt tacagaatat tatggaggtt gaggtatttg actgttgggg gattgatttt 7500 gtaggtccct tccctttgtc ttttggcaat gaatacatac tagtggttgt tgactatgtc 7560 tctaaatggg ttgaagcagt ggctaccctg cataatgatg ctaagattgt ggtaaagttt 7620 ctaaagacga acattttctc cagatttggg gtgcccagag ttttgattag tgatggaagc 7680 acacatttct gcaataataa gatacagaag gtgttgaagc aatataatgt aacacacaag 7740 gtagcatcag cttatcaccc ccaaaccaat gggcaagcag aagtgtcgaa caaggaattg 7800 aaaaagattt tagagaagac tatggcttct actagaaagg actggtccat taaactagat 7860 gatgctttat gggcgtatag gactgcattc aagactccga taggtttatc tccatttcag 7920 atggtgtatg gcaagtcttg tcacttacca gtggagatga aatataaaac atattgggcc 7980 ttgaagttgt tgaactttga tgaagccgaa tccagagaac aaaggaggct acaacttttg 8040 gagttggaag agataaaatt aactgcttat gaatcttcac agttgtacaa agaaaaaatt 8100 aaaaagtatc atgataaaaa actgctcaag agggattttc aacaaggaca acaagtgttg 8160 cttttcacct caagacttaa attgtttcct gggaagctta aatcgaaatg gtctagacca 8220 tttaccatca agaaagtccg aacatatgga gcagtggagc tttgtgatcc tcatatgggt 8280 ggtgaacgga caaaggctaa agcaatatca tggtggagct attgagagat tgaacactat 8340 tctacacttc aatccaggat aacaggacga tgcgtcaagc taatgacgtt aaccgagcgc 8400 ttacggggag gcaacccagg tctcttttta tttctatttt tcttgcattt aatttagtta 8460 gtttaattgc ttgtgattgt aaatgatttc taagcttggt tagtattgag aaaagggttt 8520 caaagtttta gtaaagagat ggatagaaaa gacttagaga aaaaattttc agttgtccat 8580 ccgctaagcg cagcccttgt gctaagtgcc atgtcttaat gcactaagca tgtgcttgct 8640 tgcgctaagc actttgacct ttcaccagtt ggctagatgg ttcagctaag cgcacatcac 8700 tgcgctaaac ctaagttctt ctctggattt gaacttcatg acttgggctt agaggagttg 8760 atgcgctaag cgcaactcct tctctgttga aaaattattg taatagcatt aagcttaatt 8820 tcctctctgg aattgaactt tcaggaattg ggcttagcag caggatacgc taagcgccaa 8880 tccttcacta ttttgaaata cttggaattg cgctaagcct ggaaccatca ctgtaagtag 8940 agcttgtttt agtgctaagc ctaacatctt aggctaagtg aaaattgcag gaccaatcag 9000 agttgcagac agtgctaagc gcgtgtcctc gcactaagct tgaatacctc tctggaattt 9060 gaaattattg aattaggctt aacgcgagag gtggcgctaa gcgcatgggc cttaaactca 9120 aatgtcatgt tggcatgcta agcgcaacta tgcgctaagt gcgccaaaca aaaatgctaa 9180 aataaaatag aactaccaat ggcagttacc atttacactt caaagctttt actcccttat 9240 gcttgtgccc acattcgtgc ttttgtgcat tttgctgcct ttgcttcaag ttattcctgc 9300 tttcttgctc tcatcttgca tttccatcac aatccaagta agttttcatg tttattttca 9360 ttttctttta taagcttaaa ccttagggta gatgatttag tgctttttag tttgcaattt 9420 tttttaggtt tagtgttttt aggttagttg ttagttaagg taggtttagg gtttacaatg 9480 taggttttag gttaggtttt tgagcccctt aggggcaatg cctgaaaaag gggtgaaaac 9540 ccgtgagtaa tttctagaaa tagcgatgaa cgtgctaagc gcacctgctg tgcttagcca 9600 gttcatcgca acttccttct aatgagtttc aatgatgagc tcgataagcg cgtttgtgcg 9660 ctaagtgaga caagtgtttt agacacttag tatttttttc aatttttgtt cagcactaaa 9720 gcctggcttc tcaggctaaa gcacaattct gtctttattt ttcaattgtt ggaataaggc 9780 taagtgcagc ttgttgtgct aagcccatgt tatgtcttag tgaggttgag ctaagcgtgc 9840 cctactgcgc taagctcaat tcctccactg ttttcaaaag tgtggattta ggataagccc 9900 agcttgttgc gctaagccta gtctatggaa aaacattttc tgagtactca cgctaagcgt 9960 gtggctatcg ggcttagccc atgagtaaat tttcataaag cgcgctaagc ccagccttct 10020 gtgctaagca cccagtccta ctttcagttt tatttttttg tttttgttga ataatcctgt 10080 tttaactctg ttgtttgatc taattctttt cagatggcat ctaggaagag aaaggcccat 10140 gcctcaacat cccaggcccg ctatgataga tccagattca catctcagga ggcctgggat 10200 cgttattcta gtgttgtcat tggcaggaaa atattacctg aaagaaatgt catgctctat 10260 tacacagagt ttgatgaatt cactgaagag ttagagagaa gaaacaggca caaggagtta 10320 acaaatttta tggatggcaa cattgatgtt gccattatga aggagttcta tgctaacctc 10380 tatgacccag aggataaatc acctaagcag gtgaggttca gaggtcattt agtgaaattt 10440 gatgcagatg ctctgaacac tttttttatg acccctgtga tc 10482 24 1857 DNA Arabidopsis thaliana 24 atgagcaatt acagtggcag ttcttctgtt gatcctgact acaacatgga tgagacagaa 60 tcgtcatctt caaggccaga gagagaacag agagaatacg aaagtttcag aaggaaagct 120 gagatagccc gaggaaagag agcgatgaga gagaggtatg agcttataga cgaagatctg 180 gaggacgagt acatgcctga acagactcgc agagctacca aacttctgca caagcccgac 240 atattgcctg ctgaggaata tgttaggctt ttcaagctga atgagttctg tagcacgagg 300 tatccttgct cgacctcact tgcacaactc ggattgttgg aagatgttca gcacctgtac 360 caaagttgtc atctggacac tttgatggct tatccgtatg tagcatatga agatgagaca 420 atacaattcc tctccacact acaagtagag ctctaccaag gtatgacctc tgatgagttg 480 gattgtgaag gattgggatt cttgcgattt tctgtgtatg gtcatgagta caggttatca 540 atcaagcgat tggaaggatt gtttgatttt cccagtggaa cgggatctaa gccaaagtat 600 gaaagagaag agttgaaaga cttgtggatc accatcggca gctctgtacc gttgaatgct 660 tccaggtcaa agagcaatca gatacgcagc cctgtcatca ggtacttcca gcgttctgta 720 gccaacgtac tctactcccg agagattaca gggactgtca ctaactctga tatggagatg 780 atcgcaatgg ccctcaaagg aactctccgc caaactaaaa atggcatgtc cctccagggt 840 gaagtcaatg acacacctct ctctatactt cttctgatcc atctgtgtgg atacaaaaac 900 tgggcggtca gcaataaccg caagagagca cgaggcgctc tgtgcatagg tggcgtggtg 960 acacctattc tgatagcttg tggagtccca ctcatttctg ctggactcga gccacgagca 1020 atggatatcg agcacctacg tcactgccaa ttcctggagt ttgcaatggt tgacgatttc 1080 cacaggttca ggtttgagca ctctacagac aggagagcta acatccttct ccctagccct 1140 gaggtcacac ggataatcga gggagataac attgatttta ggcctgagat tggacgcctc 1200 tactatgaga acgctccacc attagatgag gacgatcttc ttgaagaagc tgcttcggat 1260 gggatggatg aagatggagc agtaaagttc gacactagca tgtatcactt tgctgaacat 1320 gtacctccag cgaggcagag caagagcttg actgaagctc ataagaatta cagtaaattg 1380 cagaagtggt gcaagaagca ggacaggctg atcgccaagt gtttcaagct tctgacagac 1440 aagctgagtt gctcttcctc caccactgct attccacagg tacaacctcc tatggaaatg 1500 ccatcgagga gaattaatgc acctgcgcac aggcctgagc ttagcgagca gagagtccca 1560 catgtccagg ctaggcattc gtcattcgaa tcccgggaac acaagagaag aaggaaggct 1620 acactcactc gatctagcag cagatcacgc ctcattcact cgaggagatc actcgaccgt 1680 ggtgctggcc gcagcagaag gagagatgtc gagtttcctc agagcggtgc tggccgccac 1740 agagctgatg aggtcgagta cccatctgct ggagctgata cagaacaagg aggttcgtct 1800 atggcctggg agcaatcgca ggcagccatt gacgagcaac tacgttcatt cttcgac 1857 25 1254 DNA Pisum sativum 25 atggaatcca ggtccggagc ttcgaaaaag agaaagggcg ggaatagttc ccgtcccgtg 60 cccatacaat tcgacaccga caaatttgtc gggccaaagc aagcagtaag atatgttgct 120 ttggaaaagc gaaagatttt gccggaaaag agatttataa tcaaccctga aggcacgaac 180 cgtacattcg ccgggctgat taacagcaaa aagtgggacc ggttaatatc ccccttgaag 240 cattacgaca tcgcaacagt gcgtgagttc tacgcgaacg cactgccgaa cgacgacgag 300 ccattcacat ggacgtctag agtgtccggc cgtcctgttg cgttcgatcg ggatgcaatt 360 aaccgtgtcc tgggtgaacc gctccatctg ggagccaatg agagagacac ttaccaccaa 420 gatttaaggc ttcaccggga taccgattcg atttctactg ccctgctttt ggaagggaaa 480 tcagttgagc tgaacccatc tggggttccg atgagatacc atagggagga catgattccc 540 ttggctcaac tgatcctttt gttggttctt acaaacatca aacccaagtc tcacacttct 600 accgtgccga tcccagtggc acacttggta cacatcatcc tcacgaatat ccagattgat 660 gtggcaagga ttattgcttt ggagttgaag tccgtgattg aaagcgggct aaagtcgggg 720 gaacgagtga attgtcccct tgctttccct tgtctaatca tggctttgtg ccaacaagcg 780 agggtgaggc taccctccaa gggtcaagta aggatcccgc cggccattga tgaccgatac 840 gtggccaagt actgcaaacc gaagaatgta agaagtagtt cagctgctga ggttaccggg 900 gcttctgatg gtcctggtac ttttactcta ggatccgatc ctttccagca ggctgtctgc 960 aactacaact gggattggat ggcggcaact cagcgcgtca tgctcgatat gcacgattct 1020 atgcagctgt tacagttgca gatgcgcgac ccctccggtg agcattctat gatgtcacgt 1080 gagcagtttc tgcagcacgc tagctggcct gtggacaggc ctgtgtttgg agagggggcg 1140 ggtgctggtg caactggtgc tggtgctttt tctggtgctg ctgatgatga tgatgatgat 1200 gaggctaccg gttctgaagc cggtagtgat gagggttatg agtccttgga gggc 1254 26 564 DNA Arabidopsis thaliana 26 tgtgattcat gccagagaaa aggcaacatc aatagaagaa atgagatgcc tcagaatcca 60 atcttggaag ttgagatctt tgatgtatgg gggattgatt ttatgggtcc attcccatct 120 tcatacggta ataaatatat actggtcgcc gtagactacg tatcaaagtg ggtcgaagct 180 attgctagtc ctaccaacga tgcaaaagtt gtgctgaagt tgttcaaaac cataatcttc 240 ccaagatttg gagttcccag ggtagtaatc agtgatggcg gaaagcattt catcaacaag 300 gtttttgaga acctcttgaa gaagcatggg gtaaagcagg ttgagatctc caatagggag 360 ataaaaacaa ttctggaaaa gactgttggg attacaagga aagactggtc tgcaaagcta 420 gatgatgcat tatgggctta caggacagct ttcaagaccc ccataggtac aactcctttc 480 aatcttctct atggaaaatt atgtcatcta cccgttgagc tcgagtacaa agcaatgtgg 540 gcggtaaaac ttctgaactt tgac 564 27 600 DNA Arabidopsis thaliana 27 cttgatgctg gtgtcatcta ccctatctct gatagtactt gggtttctcc agtgcattgc 60 gtccctaaaa agggtggaat gactgttgtc aaaaatgaaa aagatgaact gatccctact 120 agaactataa ctggtcatag aatgtgcata gattatagga agttgaacgc tgcatctagg 180 aaagatcatt ttcctttacc attcattgac caaatgcttg aacgtttggc taatcatcca 240 tattattgct ttcttgatgg atacagtggt ttctttcaaa taccaattca ccctaatgat 300 caagaaaaaa ccactttcac gtgtccttat ggaacttttg cctataaaag aatgccattt 360 ggtttatgca atgctcctgc aacatttcag aggtgtatga cctctatatt ttcagactta 420 atcgaggaga tggtggaggt tttcatggac gatttttcgg tctatggccc ctctttctcc 480 tcatgtttgt tgaatcttgg cagggtattg actaggtgcg aagagacgaa tcttgttctc 540 aattgggaaa agtgtcattt catggtgaag gaaggcatag tattggacca caagatatca 600 28 192 DNA Arabidopsis thaliana 28 tttgaaatca tgtgtgatgc atcagattac gcagtaggag ctgttctagg ccagaaaata 60 gacaagaagc ttcatgtcat atattacgcc agccgaacgt tggatgacgc tcagggaaga 120 tatgcaacaa ctgagaagga gcttctagct gttgtattcg catttgagaa gttcagaagc 180 tatttggttg ga 192 29 597 DNA Pisum sativum 29 ttggatgcga gaatgattta cccgatctcg gatagtccat gggtcagtcc cgtgcatgtg 60 gttccgaaga aaggtggaaa taccgtcatc cggaatgaca aggatgaatt gatccctacc 120 aaagttgcaa cggggtggag aatgtgtatt gaatataggc ggttgaatac cgcaactcga 180 aaggaccatt ttccactccc gttcatggat caaatgctgg aaagactctc cgggcaacaa 240 tactattgtt tcttggatgg ctattccggg tataaccaaa ttgccgttga cccggccgat 300 cattaaaaga cggctttcac atgtccgttt ggagtgttcg cataccgaaa aatgtccttt 360 gggttgtgca atgcaccgac gactttccaa cgatgtgtgc aagccatttt tgccgacctt 420 aatgagaaaa caatggaagt cttcatggat gacttctcgg tatttggtgt atcctttagt 480 ttatgcttgg caaacttgaa aacggtgctt gaaagatgtg tgaagaccaa tcttgtgctt 540 aattggtaga agtgccactt catggtgacc gaggggatag tgcttggcca taaagtc 597 30 192 DNA Pisum sativum 30 tttgagctaa tgtgtgatgc gagcaactat gcaatcggag cggtattagg ccaaagaaaa 60 gagaaaaaat ttcatgcgat acattacgca agtaaagttc ttaatgaggc tcaaattaac 120 tatgccacca ctgaaaaaga attacttgcg atagtgtatg cacttgaaaa gtttaggtct 180 tatcttatag gg 192 31 581 DNA Pisum sativum 31 tgtgatagtt gccagagaag cggtgggatt ggtaagagag acgagatgtc tctccaaaac 60 atccaagagg tcgaagtatt tgattgttgg ggcatcgatt ttgtaggacc attcccccct 120 cttatggtaa cgagtatatg cttgtcgcag ttgaggcgat tgcctcacct cgggcggatg 180 cgaaaacggt aataattttt ttgaagaaaa acatattttc ccgtttcgga accccccgag 240 tgttgataag tgacggaggg tcacactttt gtaatgcacc gttggaaagc attttaaaac 300 attacggtgt atcacacaga gtggcaactc cgtatcaccc acaggctaat ggacaagccg 360 aggtctctaa tcgtgagatt aagagaattc tcgaaaaaac tgtgtcaaat tcgaaaaaag 420 agtggtcaca aaaattggat gaagcgttat gggcataccg taccgccttt aaagctccaa 480 ttgggctcac tccttttcaa ttggtgtttg gtaaaacttg ccatttgccg gtcgaattgg 540 agcacaaagc cttgtgggct ttgaaaatta ataattttga a 581 32 1362 DNA Glycine max 32 atggcctcct gtaaacaccg agctgtgccc acacccgggg aagcgtccaa ctgggactct 60 tcacgtttca ctttcgagat tgcttggcac agataccagg atagcattca gctccggaac 120 atccttccag agaggaatgt agagcttgga ccagggatgt ttgatgagtt cctgcaggaa 180 ctccagaggc tcagatggga ccaggttctg acccgacttc cagagaagtg gattgatgtt 240 gctctggtga aggagtttta ctccaaccta tatgatccag aggaccacag tccgaagttt 300 tggagtgttc gaggacaggt tgtgagattt gatgctgaga cgattaatga tttcctcgac 360 accccggtca tcttggcaga gggagaggat tatccagcct actctcagta cctcagcact 420 cctccagacc atgatgccat cctttccgct ctgtgtactc cagggggacg atttgttctg 480 aatgttgata gtgccccctg gaagctgctg cggaaggatc tgatgacgct cgcgcagaca 540 tggagtgtgc tctcttattt taaccttgca ctgacttttc acacttctga tattaatgtt 600 gacagggccc gactcaatta tggcttggtg atgaagatgg acctggacgt gggcagcctc 660 atttctcttt agatcagtca gatcgcccag tccatcactt ccaggcttgg gttcccagcg 720 ttgatcacaa cactgtgtga gattcagggg gttgtctctg ataccctgat ttttgagtca 780 ctcagtcctg tgatcaacct tgcctacatt aagaagaact gctggaaccc tgccgatcca 840 tctatcacat ttcaggggac ccgccgcacg cgcaccagag cttcggcgtc ggcatctgag 900 gctcctcttc catcccagca tccttctcag cctttttccc agtgaccacg gcctccactt 960 ctatccacct cagcacctcc atacatgcat ggacagatgc tcaggtcctt gtaccagggt 1020 cagcagatca tcattcagaa cctgtatcga ttgtccctac atttgcagat ggatctgcca 1080 ctcatgactc cggaggccta tcgtcagcag gtcgcctagc taggagacca gccctccact 1140 gacagggggg aagagccttc tggagccgct gctactgagg atcctgccgt tgatgaagac 1200 ctcatagctg acttggctgg cgctgattgg agcccatggg cagacttggg cagaggcagc 1260 tgatcttatg ctttaatgtt ttcttttata ttatgtttgt gttctctttt atgttttatg 1320 ttatgttttt atgtagtctg tttggtaatt aaaaagaggt ag 1362 33 192 DNA Glycine max 33 tttgagttga tgtgtgacgc gagcgattat gctataggtg cagtgcttgg acaaaggaag 60 ggcaaaattt ttcatgctat ctactacgcc agcaaagttt taaatgatgc acaggttaac 120 tatgctacca cagaaaaaga aatgttggca attgtttatg cacttgaaaa gttcaaatct 180 tatttggtag gc 192 34 597 DNA Glycine max 34 ttggaggttg ggctcatata ccccatctct gacaacgctt gggtaagccc agtacaggtg 60 gttcccaaga aaggtggaat gacagtggta caaaatgaga ggaatgactt gataccaaca 120 cgaacagtca ctggctggcg aatgtgtatt gactatcaca agctgaatga agctacacgg 180 aaggaccatt tccccttacc tttcatggat cagatgctgg agagacttgc agggcaggca 240 tactactgtt tcttggatgg atactcggga tacaaccaga tcgcggtaga ccccatagat 300 caggagaaga cggtctttac atgccccttt ggcgtctttg cttacagaag gatgtcattc 360 gggttatgta atgtaccagc cacatttcag aggtgcatgc tgaccatttt ttcagacatg 420 gtggagaaaa gcatcgaggt atttatggac gacttctcgg tttttggacc ctcatttgac 480 agctgtttga ggaacctaga aatggtactt cagaggtgcg tagagactaa cttggtactg 540 aattgggaaa agtgtcattt tatggttcga gagggcatag tcctaggcca caagatc 597 36 150 DNA Glycine max 36 cctaaaatac tacaacgaca tgattggtgt tttaggataa ttgactgaaa aacctattat 60 caatttggcg ccgttgccaa ttgggtgttt gtttgttaca tttgagattt cagacttgct 120 tagatcaagt tctttttcaa ttttcttttt 150 37 11 DNA Glycine max 37 tggcgccgtt g 11 38 15 DNA Glycine max 38 tggcgccgtt gccgg 15 39 27 DNA Glycine max 39 tttttggcgc cgttgtcggg gattttg 27 40 9 DNA Glycine max 40 tttggggga 9 41 16 DNA Glycine max 41 tttaatttgg gggatt 16 

What is claimed is:
 1. An isolated nucleic acid molecule, wherein said nucleic acid molecule encodes at least a portion of a plant retroelement and comprises a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which is a plant retroelement primer binding site and which has more than 95% identity to SEQ ID NO 2, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which is at least a portion of a plant retroelement envelope sequence and which has more than 50% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters; (c) a nucleic acid sequence which is at least a portion of a plant retroelement gag sequence and which has more than 50% identity to SEQ ID NO 7, wherein said identity can be determined using the DNAsis computer program and default parameters; (d) a nucleic acid sequence which is at least a portion of a plant retroelement integrase sequence and which has more than 70% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters; (e) a nucleic acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and which has more than 70% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters; (f) a nucleic acid sequence which is at least a portion of a plant retroelement protease sequence and which has more than 50% identity to SEQ ID NO 13, wherein said identity can be determined using the DNAsis computer program and default parameters; (g) a nucleic acid sequence which is at least a portion of a plant retroelement RNAseH sequence and which has more than 70% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters; (h) a nucleic acid sequence which is at least a portion of a plant retroelement sequence and which has more than 50% identity to SEQ ID NO 17, wherein said identity can be determined using the DNAsis computer program and default parameters; (i) a nucleic acid sequence which is selected from the group consisting of: SEQ ID NO 2; SEQ ID NO 5; SEQ ID NO 7; SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 13; SEQ ID NO 15; and SEQ ID NO
 17. (j) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement envelope sequence and has more than 30% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters; (k) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement gag sequence and has more than 30% identity to SEQ ID NO 8, wherein said identity can be determined using the DNAsis computer program and default parameters; (l) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement integrase sequence and has more than 75% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters; (m) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement reverse transcriptase sequence and has more than 79% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters; (n) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement protease sequence and has more than 55% identity to SEQ ID NO 14, wherein said identity can be determined using the DNAsis computer program and default parameters; (o) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement RNAseH sequence and has more than 90% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters; (p) a nucleic acid sequence which encodes an amino acid sequence which is at least a portion of a plant retroelement sequence and has more than 40% identity to SEQ ID NO 18, wherein said identity can be determined using the DNAsis computer program; (q) a nucleic acid sequence which encodes an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; (r) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence selected from the group consisting of: SEQ ID NO 4; SEQ ID NO 6; SEQ ID NO 8; SEQ ID NO 10; SEQ ID NO 12; SEQ ID NO 14; SEQ ID NO 16; and SEQ ID NO 18; and (s) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); a nucleic acid sequence of (e); a nucleic acid sequence of (f); a nucleic acid sequence of (g); a nucleic acid sequence of (h); a nucleic acid sequence of (i); a nucleic acid sequence of (j); a nucleic acid sequence of (k); a nucleic acid sequence of (l); a nucleic acid sequence of (m); a nucleic acid sequence of (n); a nucleic acid sequence of (o); a nucleic acid sequence of (p); a nucleic acid sequence of (q); and a nucleic acid sequence of (r).
 2. A seed comprising a nucleic acid of claim
 1. 3. A plant comprising a nucleic acid of claim
 1. 4. A nucleic acid molecule of 1, which comprises gag, pol and env genes and which comprises adenine-thymidine-guanidine as the gag gene start codon.
 5. A nucleic acid molecule of claim 2, which further comprises SEQ ID NO
 4. 6. An isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule encodes at least a portion of a plant envelope sequence and comprises a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 5, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes SEQ ID NO 5; (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 6, wherein said identity can be determined using the DNAsis computer program and default parameters; (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 6; (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 6; and (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).
 7. A plant cell comprising an isolated nucleic acid molecule of claim
 6. 8. A plant retroviral envelope protein comprising an amino acid sequence encoded by a nucleic acid molecule of claim
 6. 9. A method to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroviral envelope protein of claim 8 to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.
 10. An isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule encodes at least a portion of a plant integrase sequence and comprises a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 9, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes SEQ ID NO 9; (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 10, wherein said identity can be determined using the DNAsis computer program and default parameters; (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 10; (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 10; and (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).
 11. A plant cell comprising an isolated nucleic acid molecule of claim
 10. 12. A plant retroviral integrase protein comprising an amino acid sequence encoded by a compound of claim
 10. 13. A method to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroviral integrase protein of claim 12 to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.
 14. An isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule encodes at least a portion of a plant reverse transcriptase sequence and comprises a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 11, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes SEQ ID NO 11; (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 85% identity to SEQ ID NO 12, wherein said identity can be determined using the DNAsis computer program and default parameters; (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 12; (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 12; and (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).
 15. A plant cell comprising an isolated nucleic acid molecule of claim
 14. 16. A plant retroviral reverse transcriptase protein comprising an amino acid sequence encoded by a compound of claim
 14. 17. A method to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroviral reverse transcriptase protein of claim 16 to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.
 18. An isolated nucleic acid molecule of claim 1, wherein said nucleic acid molecule encodes at least a portion of a plant RNAseH sequence and comprises a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 90% identity to SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes SEQ ID NO 15; (c) a nucleic acid sequence which encodes an amino acid sequence which has greater than 95% identity to SEQ ID NO 16, wherein said identity can be determined using the DNAsis computer program and default parameters; (d) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 16; (e) a nucleic acid sequence which encodes an allelic variant of SEQ ID NO 16; and (f) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); a nucleic acid sequence of (d); and a nucleic acid sequence of (e).
 19. A plant cell comprising an isolated nucleic acid molecule of claim
 18. 20. A plant retroviral RNAseH protein comprising an amino acid sequence encoded by a compound of claim
 18. 21. A method to impart agronomically-significant characteristics to at least one plant cell, comprising: contacting a plant retroviral RNAseH protein of claim 18 to at least one plant cell under conditions sufficient to allow a nucleic acid molecule to enter said cell, wherein said nucleic acid molecule encodes an agronomically-significant characteristic.
 22. An isolated retroelement comprising a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 95% identity to SEQ ID NO 2; wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which is SEQ ID NO 2; (c) a nucleic acid sequence which encodes amino acid sequence SEQ ID NO 4; and (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).
 23. A plant retroelement of claim 22, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic.
 24. A plant retroelement of claim 23, wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content.
 25. A plant retroviral particle of claim 23, wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.
 26. An isolated plant retroviral particle comprising an isolated retroelement of claim
 22. 27. A seed comprising comprising a plant retroelement of claim
 22. 28. A plant comprising a plant retroelement of claim
 22. 29. A plant of claim 28, which plant is selected from the group consisting of: soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory, pepper, melon; cabbage; oat; rye; cotton; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; pears; peaches; banana; palm; cocoa; cucumber, pineapple; apricot; plum; sugar beet; lawn grasses; maple; triticale; safflower; peanut; and olive.
 30. A plant of claim 29, which is soybean.
 31. A method to transfer nucleic acid into a plant cell, comprising contacting a plant retroelement of claim 22 with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell.
 32. A method to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroelement of claim 23 with at least one plant cell under conditions sufficient to allow said plant retroelement to enter said cell.
 33. A method of claim 32, wherein the plant retroelement is contacted with said cell via a plant retroviral particle of claim
 34. 34. A plant retroviral particle comprising a plant-derived retrovirus envelope protein.
 35. A plant retroviral particle of claim 34, which further comprises a plant retroviral protein selected from the group consisting of: plant-derived integrase; plant derived reverse transcriptase; plant-derived gag; and plant-derived RNAseH.
 36. An isolated plant retroviral particle comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence comprising (i) a nucleic acid sequence which encodes at least one plant retroviral envelope protein, and (ii) a nucleic acid sequence which has more than 60% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; SEQ ID NO 15; SEQ ID NO 26; SEQ ID NO 27; SEQ ID NO 28; SEQ ID NO 29; SEQ ID NO 30; and SEQ ID NO 31, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence (a); (c) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid sequence of (a); and (d) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); and a nucleic acid sequence of (c).
 37. A plant retroelement of claim 36, wherein said nucleic acid sequence as described in (a) comprises a nucleic acid sequence of claim
 6. 38. A plant retroelement of claim 38, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic.
 39. An isolated retroviral particle comprising a plant retroviral protein encoded by a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence which has more than 80% identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15, wherein said identity can be determined using the DNAsis computer program and default parameters; (b) a nucleic acid sequence which encodes a nucleic acid selected from the group consisting of: SEQ ID NO 9; SEQ ID NO 11; and SEQ ID NO 15; (c) a nucleic acid sequence which encodes an amino acid sequence encoded by a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); (d) a nucleic acid sequence which encodes an allelic variant of an amino acid sequence encoded by a nucleic acid selected from the group consisting of: a nucleic acid sequence of (a); and a nucleic acid sequence of (b); and (e) a nucleic acid sequence fully complementary to a nucleic acid sequence selected from the group consisting of: a nucleic acid sequence of (a); a nucleic acid sequence of (b); a nucleic acid sequence of (c); and a nucleic acid sequence of (d).
 40. A plant retroviral particle of claim 39, which further comprises at least one nucleic acid sequence which encodes at least one agronomically-significant characteristic.
 41. A plant retroviral particle of claim 40, wherein the agronomically-significant characteristic is selected from the group consisting of: male sterility; self-incompatibility; foreign organism resistance; improved biosynthetic pathways; environmental tolerance; photosynthetic pathways; and nutrient content.
 42. A plant retroviral particle of claim 40, wherein the agronomically significant characteristic is selected from the group consisting of: fruit ripening; oil biosynthesis; pigment biosynthesis; seed formation; starch metabolism; salt tolerance; cold/frost tolerance; drought tolerance; tolerance to anaerobic conditions; protein content; carbohydrate content (including sugars and starches); amino acid content; and fatty acid content.
 43. A method to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle of claim 39 to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.
 44. A method to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle of claim 40 to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.
 45. A method to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle of claim 36 to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.
 46. A method to transfer nucleic acid into a plant cell, comprising contacting a plant retroviral particle of claim 37 to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.
 47. A method to impart agronomically-significant characteristics to a plant, comprising contacting a plant retroviral particle of claim 38 to at least one plant cell under conditions sufficient to allow said nucleic acid to enter said cell.
 48. An isolated nucleic acid having at least 20 contiguous nucleotides of the sequence shown in SEQ ID NO
 17. 49. An isolated nucleic acid, comprising, in the 5′ to 3′ direction: a first nucleotide sequence comprising SEQ ID NO:1, or the complement thereof; a second nucleotide sequence having at least 95% identity to SEQ ID NO:2, or the complement thereof; a third nucleotide sequence selected from the group consisting of a nucleotide sequence having at least 70% identity to SEQ ID NO:9, the complement thereof, a nucleotide sequence that encodes a polypeptide having at least 75% identity to SEQ ID NO:10, and the complement thereof; a fourth nucleotide sequence selected from the group consisting of a nucleotide sequence having at least 70% identity to SEQ ID NO:11, the complement thereof, a nucleotide sequence that encodes a polypeptide having at least 79% identity to SEQ ID NO:12, and the complement thereof; a fifth nucleotide sequence selected from the group consisting of a nucleotide sequence having at least 70% identity to SEQ ID NO:15, the complement thereof, a nucleotide sequence that encodes a polypeptide having at least 90% identity to SEQ ID NO:16, and the complement thereof; a sixth nucleotide sequence selected from the group consisting of a nucleotide sequence having at least 50% identity to SEQ ID NO:5, the complement thereof, a nucleotide sequence that encodes a polypeptide having at least 30% identity to SEQ ID NO:6, and the complement thereof; a seventh nucleotide sequence comprising SEQ ID NO:4, or the complement thereof; and an eighth nucleotide sequence comprising SEQ ID NO:3, or the complement thereof. 